myPresto 4.2
Contents
1. Prepare a file desi gnati ng the di stance restrai nt between atons DI STANcerestrai n Use restraint di stance between atons NCREad Do not apply Default READ Appl y UN TO stance lO unit of distance desi gnati on file 17 Q Default AQ NAMED st ance Nene of file for desi gnati ng d stance between atons 80 chars nax O O O Desi gnati on of di hedral ang e restraints DI FELFal restrai n Use dihedral angl e restraints NCREad Do not appl y Default READ Appl y UN TCH IO unit of dihedral angle restraint desi gnati on file 18 O Def au AQ NAMED Nane of dihedral angl e restraint desi gnati on file 80 chars nax OO0 QT ndi cates end of EXE group i nput myPresto 4 2 10 L212 DE gt AM ysis group Here you desi gnate the net hod convergence condi ti ons cal cul ati on resul t output energy terns used in cal cul ati on and the boundary restrai nt condi ti ons which are needed for energy nhni mzati on A most all desi gnati ons rel ati ng to energy cal cul ati on are the sane as those for the EXE gt M group O O 0 Anal ysis nethod O O 0 0 Mthod to anal yze a si ng e structure It anal yzes the coordi nate file desi gnated by the NPUTgroup M QATI oncheck Test the abnor nal gene associ ated ength abnornal bi ndi ng angl e and van der V al s contact NO I Def aul t YES FCRCEAnal ysis Output the force applied to each atomi n the atomdata file It is required to d2. 5th chai n Transition of RSD average structure RM6Dof each at omand x y and z conponent s of RSD etc are output to the standard output file Mi Standard output file ana 1 out NFCRMATI ON gt ANALYS CALGLLATE AVERAGE AND FLUCTUATI ON NUMBER CF SELECTED DATA 100 RSD DATA NUMBER OF ATOS CF FIRST CAIN 2008 NUMBER CF ATOS FCR EEST FIT 1049 AVERACE ALL ATOM 4 2578762709675724 SELCTED ATOM 0 41109270952623123 SD ALL ATOM 1 3583200792547043 SELCTED ATOM 3 94575716745282287E 2 EACHATOMDNTA x y and z coordi nates of average structure RSD x y and z conponents of RMED 1N GY 1 1 1 16 58385 5 37864 14 14423 0 12539 O 7546969E 01 0 8198197E 01 0 5748686E 01 2 HL GY 1 1 1 16 96925 5 08163 14 94453 0 04053 O 1919956E 01 0 3203947E 01 0 1574088E 01 myPresto 4 2 24 Transition of RMD is output to the pl ot data The Ist col unm shows the elapsed ti nel PSEQ the 2nd col unm shows RSO At first superi npose the coordi nates of trajectory of an atomdesi gnated by the desi gnati on of superi nposi ng atomon the reference coordi nate and cal cul ate and output RMSD of all atons Then after RM6D PART superi npose the traj ectory coordi nates of an atomdesi gnated by the superi nposi ng at omand out put the val ue of RVBDof onl y the at omdesi gnated Nornal y the val ues after ZRVBD PART are used for anal yses M Plot data rnsd pl ot data RMSD ALL 0 RMD of all atons 0 200000
3. ALLB CALC 100 0 NO CALC YES RESA CONS CALC Apart of protein fi xed by position restraint and a systemi ncl udi ng netal atons and i gand coordi nated to it surrounded by CAP water are cal cul ated Wth regard to myPresto 4 2 22 the system the 1st chain is protein the 2nd to 4th chain is Ca ion the 5th chain is Znion the 6th chain is ligand the 7th chain or later is water nol ecul e MD of the systemperforns the nd inp as a control file Posi ti on restrai nt fil eMall res is desi gnated as fol ows The li gand nol ecul e and water nol ecul e can nove freely in CAP potential MW Posi ti on restraint desi gnati on file Mall res Thi s coordi natetraj ectory fil eis anal yzed Transi ti ons of devi ati ons RSD from the ref erence coordi nat es of coordi nates traj ectory at each step and averagestructure are obtai ned Transitions of RSD are out put to the standard output and plot data The average structure is output to a file desi gnated by NAMECO lil Control file ana l i np FORM NAMETO initial tpl Topol ogy file of the system POB NAMECO initial pdo PLB file of the system PLB NAMERE initial pdb Reference coordi nates MD traj ect cor Goordi nates trajectory file cal cul ating MD a4 Desi gnati on of types of trajectory file DETAIL Desi gnati on of standard out put 1 Step i nterval of analysis STARTT 0 0 O Start tine of anal ysi sf PSEC ENDTI M 20 0 End ti ne of anal ysis
4. nunber a file desi gnated by NAMEBS i s not oaded and all atons of the lst chai nthe 1st chai n are used If a positi ve nunber 511 is designated thefileisl oaded and atons of nul ti pl e chai ns can be desi gnated However a desi gnat ed at omnust i ncl ude an atomof the lst chai n O O E Analysis data output NAMEPL Nene of a plot data file UN TPL IO Uni t of a plot data file 62 I Def aul t NAMEAT Nene of an atomdata file UN TAT IO Uni t of atomdata file 63 LI Def aul t O O Desi gnati on of energy trajectory cal cul ati on METHOD Thi s desi gnates types of energy traj ectory MN_ Energy traj ectory anal ysis of the result of nani mzati on Def aul t MD Energy trajectory anal ysis of M result myPresto 4 2 The follow ng is enabled onl y when MTHDMN STARTLoop Loop nunber to start an anal ysis O I Def aul t ENDLOQY Loop nunter to end an anal ysi s 10000 I Def aul t The foll ow ng is enabl ed onl y when METHCD MD NTERVal Step interval to performan anal ysi s al I Def aul t STARTTi nef Ti ne to start an anal ysi s PSEC O I Def aul t ENDII Ma Ti ne to end an anal ysi s PSEC 10000 I Def aul t O O O Control paraneter for FORCEAnal ysi s YES Desi gnate the sane paraneter as generating trajectory 00 00 Interaction CUTOFF nethod QUIMEThod Interacti on CUTCFF net hod RESC Resi due base cutoff Default Gl cul ates the i nteracti o
5. trajectory anal ysis myPresto 4 2 L211 EX INPUT group As the MNM calculation The INPUT group desi gnates external files li ke the topology initial coordinates and files desi gnati ng atons to be restrained or noni tored Refer to Al nput Qut put file at the end of the user nanual ANALI SI S can perf ormt he fol ow ng desi gnati ons Itens desi gnated i n the INPUT group O O O Desi gnati on of topol ogy of system O O O Desi gnati on of coordinates of system O 0 O Desi gnati on of fixed atons and free atons O O O Desi gnati on of CAP potenti al O 0 O Desi gnati on for RMSD cal cul ati on O 0 O Desi gnati on of posi ti on restrai nt O O O Desi gnati on of restraint di stance between atons O O O Desi gnati on of dihedral angl e restrai nt OO0 QT O O O Desi gnati on of topol ogy of system TCPQ Oyf Fornat of topol ogy file O NCREad No topol ogy file input Default FORMX t ed Fornatted ASG file B Wry Binary file UN TTQpol ogy 10 uni t of topol ogy fil e AQ 10 Def aul t NAMETQpol ogy Topol ogy nane 80 chars nax When TPQ Qy FOM BI NA Desi gnati on of coordi nates of system Como nate Fornat of 3 di nensi onal coordi nate file in PLB fornat NCREad O No coordi nate input Def aul t PLB POB file fornat Bl Wry Binary file UN T Oor di ante UN TGOor di nate 10 unit of coordi nate file AQ 11 Def aul t NAMECOor di nat ex Coor di nate file nan
6. 0 0 7820804 0 4000000 1 1031598 0 6000000 1 3053278 0 8000000 1 4847158 19 7999992 6 1756648 20 0000000 6 2183821 RMSD PART RMD of desi gnat ed 0 2000000 0 2947671 0 4000000 0 3071040 0 6000000 0 3031894 0 8000000 0 3269165 myPresto 4 2 B ank space 25 myPresto 4 2 myPresto 4 2 cosgene ANALYSIS
7. ALHYD Hydrogen bonds CALC Cal cul at e Def aul t NOCAI c Do not cal cul ate Wen not usi ng an interaction table The above CAL VI5 CLAE15 and CALHYDar e set to NOCALG and CALVON CALESN and CALH5N are set to ALC CALVSN 1 5 van der V al s NOCAI c Do not directly cal cul ate 1 5 van der Waals Def aul t CALC Cal cul ate CALE5N 1 5 el ectrostati c interaction NOCA c O Do nt drectl y cd cu ate 1 5 d ecrostati c interaction Def au t CALC Cal cul ate CALP5N Hydrogen bonds NOCA c Do not directly cal cul ate hydrogen bonds Default CALC Cal cul ate 00 0 00 Restraint potential Restraint potential settings are all set to NOCALC no cal cul ati on by default Pl ease set the correspondi ng energy cal cul ati on termwhen usi ng soft core soft repulsi on for CAP restraint position restraint di stance angl e torsi on restrai nt or van der V als repulsion etc In addition ordinarily you should desi gnat e the appl i cable atons for these potentials see the secti on on DEJ NPUT and input paraneters where they are requi red for force constants etc Al of these restraint potenti al s are added to the potential energy termof the enti re system myPresto 4 2 16 CALPSR Posi ti on restrai nt NXA c Do not cal cul ate Def aul t CALC Gl cul ate Desi gnate the foll ow ng in the EXE NPUT phase POSI TI CN READ NAMEPO Posi ti on restrai nt desi gnati on file REFCOORD PLB NAMERE
8. PSEC UN TBS 61 fl lOunit nunber of NAVEBS NAMEBS set bst_1 bst Atomdesi gnati on used for superi nposi ng coordi nat es BESTFI YES Superi nposes the coordi nates FLUCTU YES Cal cul ates the fl uctuati on NAMEPL rnsd plot data Plot data of RMSD QUT EXE gt CUTPUT COCRO NATE PLB NAMECO nean pdb Average structure to be out put QUT EXE gt END myPresto 4 2 RMSD i s cal cul ated by superi nposi ng the reference coordi nate to the coordi nates of thetrajectory file If no superi nposi ng of atons is desi gnated all tons of the 1st chai n are desi grated It is preferable to desi gnate so that hydrogen atomi s not desi gnat ed f or superi nposi ng and net al atons f romt he 2nd to 5th chai n are used for superi nposi ng Therefore prepare the fol ow ng atomdesi gnati on file to desi gnate In the second li ne cancel the desi gnati on of all atons by FI X tenporari y and new y desi gnate atons wth the li nes after that Atons of the Ist chai n nast be incl uded i n the desi gnati on llt omdadesi gnati on file setbst_1 bst SETBST gt LI ST FIX 1 137 Rel ease atomdesi gnati on FREE 1137 Desi gnate all atons wth an atomnane starti ng fromC FREE 1 137 Desi gnate all atons wth an atomnane starting fromN FREE 1 137 Desi gnate all atons wth an atomnane starti ng fromQ 1 137 Desi gnate all atons wth an atomnane starting f romS 1 1 Desi gnate all atons of fromthe 2nd to
9. Ref erence coordi nate file CALDSR di stance restrai nt NAc Do not cal cul ate Def aul t CALC Gl cul ate Desi gnate the foll ow ng in the DEH NPUT phase O STANcer est rai n READ NAMED stance Li stance restraint desi gnati on file CALDHR di hedral restrai nt NXA c Do not cal cul ate Def aul t CALC Gl cul ate Desi gnate the foll ow ng in the EXE NPUT phase DI HEDRal restrain READ NAMEDH Li hedral restraint desi gnati on file CALREP si npl e repul si on NXA c Do not cal cul ate Def aul t CALC Gl cul ate CALCAP CAP restrai nt NXA c Do not cal cul at e Def aul t CALC Gl cul ate Desi gnate the foll ow ng in the EXEX NPUT phase SETBO ndary READ NAMEBOundary CAP boundary desi gnati on file Paraneters necessary for restraint potential TEMPERat ure Temperature used for restrai rt K Position Dstance Repision Dhedd 300 0 Befaut AQ VETESR Li stance restraint vei ght myPresto 4 2 17 1 0 Def aul t VETPSR Posi ti on restraint vei ght 3 0 O Def aul t VETDHR Li hedral restraint vei ght 10 0 Def aul t Si npl e repu si on paraneters VETREP Si npl e repul si on vei ght 1 0 Def aul t REPSCA ef Van der V al s radi us scale f actor 1 0 Def aul t REPLELEa Pernnssi bl e tol erance 1 0 Def aul t CAP restrai nt paraneters Wth CAP restrai nt you nost desi gnate the CAP center radi us and the repul si on type a
10. al cul ate CALI MProper nproper torsi on cal cul ati on CA C Cal cul ate Default NOCA c Do not cal cul ate CALVIA 1 4 van der V al s cal cu ati on CALC Cal cul ate Def aul t NOCA c Do not cal cul ate CALE1A 1 4 el ectrostati c interaction cal cul ati on CALC Cal cul ate Def aul t NOCA c Do not cal cul ate 00 0 0 0 1 5 interaction swtch This changes the swtch desi gnati on when cal cul ati ng usi ng CUTCFF cal cul ati on usi ng an i nteracti on table and when cal cul ating all 1 5 interactions for all atons wthout usi ng CUTCFF direct cal cu ation The default setting is to use CUTCFF Nornally default all of the following are calculated van der V als 1 5 el ectrostati c interaction and hydrogen bonding Although it is extrenaly rare pl ease use thi s onl y when you do not wish to calcul ate a certain interaction If you use a force fi el d whi ch does not i ncl ude hydrogen bonds 12 10 Potential hydrogen bonds are not cal cul ated regardless of the val ue of the swtch CALHYD Wen usi ng an i nteracti on tab e usi ng CUTOFF The fol ow ng CA VI5 CLAE15 and CALHYD are set to CALC and CALV5N CALESN and CAHN are set to NOCALC Def aul t myPresto 4 2 CALVI5 1 5 van der V al s CALC Cal cul at e Def aul t NOCA c Do not cal cul ate CALE15 1 5 electrostatic i nteracti on cal cul ati on CALC Gal cu ate Default Mandatory wth PME FMM NOCA c Do not cal cul ate C
11. c is speci fi ed by the control file as the MN MDcal cul ati on Later see the chapter cosgene in the user nanual cosgene lt control file output L2 Input data creati on 121 Control file Acortrol file is conpri sed of the fol ow ng groups Each group i s terminated wth QU T EXE gt I NPUIgroup The DE NUT group desi getes the pri nary i npt file nanes DE gt ANN ysisgroup The BEAN ysi s group desi gnates the options of group trajectory anal ysi s EX QUIPUTgroup The EXE gt QUIPUM group designates output for final results EX END EXE END indi cates the end of the control file myPresto 4 2 FLUCTU NAMEPL QUT EXE gt CUTPUT FORM NAMETO initial tpl Topology file PLB NAMECO initial pdb QPDBfile PLB NAMERE initial pdo Reference coordi nates MD traj ect cor DETAI L 1 0 0 20 0 61 setbst 1 bst Goordi nate traj ectory file for MD cal cul ati on Desi gnates the types of trajectory files Desi gnates standard out put D Anal ysis step i nter val Anal ysis start ti ne PSEC Anal ysi s end ti ne PSEC O 1 O unit nunber of NAMEBS Atomdesi gnati on used for superi nposi ng coordi nates Superi nposes coordi nat es YES rnsd pl ot data Cal cul ates fl uctuati on Plot data of RMSD CooRD NATE PLB NAMECO mean pdb Average structure to output QUT EXE END Exanpl e of control files in the case of
12. cad e atons BOUNDS y Boundary condi ti on type NO O No boundary Default PERI Peri odi c boundary condi ti ons ELLI PSoi d Hl i psoi d boundary SPHERE Sphere boundary O O O O Boundary condition si ze setti ng For peri odi c boundary condi ti ons This sets the length al ong the X Y and Z axes of the unit cell LXCELL 40 0 Def aul t LYCELL 40 0 Def aul t LZCELL 40 0 Def aul t For an ellipsoid Thi s desi gnates the radi us in the X Y and Zdi recti ons assunnngthe naj or and mnor axes of the elli psoi d are ali gned wth the XYZ coordi nati on di recti ons ELLI PA 30 0 O Def aul t ELLI PB 30 0 O Def aul t ELLI PG 30 0 Def aul t For a sphere This desi gnates the radi us of the sphere RAD US 30 0 q BDefaut myPresto 4 2 19 000 UL ST If you add the conmand LIST current paraneter settings wll be displayed No paraneters 0000 QT Thi s indicates the end of EXE group i nput No paraneters myPresto 4 2 20 B ank space myPresto 4 2 2 Sanple cal cul ati ons lg Control file na i np NAMETO initial tpl NAMECO initial pdb NAMEPO Mall res NAMERE initi aO pdb NAMEBO M dock capbc NAMESH initial shk 5000 ODO CPUTI M 3600000 ODD 20 2 ODO 200 LOGOR LETA NO 100 traject cor Coordi nates trajectory file SI NG 200 traject ene Energy traj ectory file ASC traj ect eto ASC CANON CAL 300 ODO 300 ODO
13. const ant s OL NCREad Do not use CAP READ O Ue CAP UN TBOundar y 1O unit of CAP desi gnati on file AQ 14 Def aul t NAMEBOundar y Nane of CAP desi gnati on fil e 80 chars mx OD O O O Desi grati on for RMD cal cul ati on when usi ng MN or MD REFCOO di nat e Referencefile Thecoord natefileinPOBfornat wi chserves as the basi s NCREad Do ret use Default PLB e UN TREf coordi IO uni t of reference file Al 15 Default NAMEREF coor di Reference file nane 80 chars nax O O O Desi gnati on of position restrain You mst prepare the follow ng two files in order to use positi on restraint A restraint desi gnati on fil e whi ch desi gnates the atons to be restrai ned and i nf ornati on about the force constant Reference file in PLB fornat listing coordi nates to be restrai ned myPresto 4 2 REFCOO di nate Reference file sane as for RSD Off NCREad Do not use Def aul t PLB be UN TREf coordi 1O Uni t of reference file AD 15 Def aul t NAMEREF coor di Reference file nane 80 chars nax OD PCBI TI onrestrai n Desi gnati on of appli cabl e atons and force constant etc OD NCREad Do not use Default READ Use UN TPGsi tion IO unit of file desi gnati ng atons to be constrai ned 16 I Default AQ NAMEPGsi ti on Nre of file desi gnati ng atons to be constrained 80 chars mx O O O O Desi gnati on of restraint di stance betveen atons
14. e 80 chars max Vihen COCRD4 PORAI BI NAJ O 0 O Desi gnati on of fixed atons and free atons Wth fixed atom designation the designated atomis not subject to MNM cal cul ati on and is handl ed as a poi nt where a force field is applied Free atons are those atons subj ect to the nornal MN IM cal cul ati on You can desi gnate the nos myPresto 4 2 of atons to be fixed or desi gnate radii R1 and R2 relati ve to a specific center or desi gnat e atons so the di stance Rf romthe center satisfies RL R R2 A control file is necessary to do this Free atomdesi gnati on is done i n the sane way If no desi gnati on is nade all atons in the systemare handl ed as free atons SETVARI abl es Fornat of fi xed free atomdesi gnati on file AQ NCREad No fi xed atomdesi gnati on Default READ Desi gnate fi xed atons UN TVAri bl es 1O unit of fi xed atomdesi gnati on file AT 13 Def aul t NAMEVAri abl es Nane of file desi gnati ng fi xed atons 80 chars nax DO O O Desi gnati on of CAP potenti al AP Thi s desi grates the ators to wi ch GP potential is applied coord nates of the GP ceter and corstarts for rad us and force You can desi gate atons in the GP desi nation file and irfornati on li ke center coord nates can be desi gated either in the GP desi gati on file or inthe cotrd file Hwveve cortrd fileinot WII take priority SETBOuUndar y Desi gnat es at ons f or appl yi ng CAP potenti al and CAP radi us and f orce
15. esi gnate the energy paraneter as MNM FMPM is not support ed NO LI Def aul t YES ELECTRostatic Cal cul ate 1 5 el ectrostati c i nteracti on appl i ed to each at omand output to the atomdata file Adielectric constant nost be desi gnat ed NO I Def aul t YES Guti on Prepare a trajectory file that is enpty now It is required to perform an input desi gnati on NAMETR of traj ectory file after nenti oned fornal y DO O 0 O A nethod to anal yze a trajectory file ENERGrtraj ectory Cal cul ate t he ener gy traj ectory and cal cul ate and out put the average and standard devi ati on i n the pl ot data file NO I Def aul t YES DI STANceanal ysis This cal cul ates a trajectory of an atonnc di stance f roma traj ectory file of coordi nate and outputs to aplot data file It is required myPresto 4 2 11 to load a control file of a distance restraint NO LI Def aul t YES DI FELFal anal ysis Thi s cal cul ates adi hedral angl etraj ectoryfromatraj ectory file of coordi nates It is requi red to oad a control file of adi hedral angle restrai nt NO I Def aul t YES FLUCTUat i on O Thi s cal cul ates a fl uctuati on of an average structure RSD and coor di nates f roma coordi nate traj ectory file and out puts it toa pl ot data file An average structure is output in the OUTPUT secti on NO LI Def aul t YES O00 Gl cul ati on result output desi gnati on LOG CRnat Fornat o
16. f standard i nput AQ SHCRE O Si mol e output wthin 80 chars in 1 line Default DETAI Detail ed output w thi n 80 chars inl line Add each energy O O Structure superi nposi ng cal cul ati on desi gnati on BESTFI t Thi s superi nposess the Ist chai n of the systemrd ati ve to the reference structure or atons desi gnat ed by acoordi nat e superi nposi ng desi gnati on file This is designated when fluctuation of average structure coordi nate or RMD is cal cul ated FLUCTLEti orf YES NO Do not calculate Def aul t YES Gl cul ate O Gauti on For the reference structure you nast desi gnate REFCOCRD and NAMERE i n the DE NPUT phase AQ O O O Analysis data i nput O00 0 0 Trajectory file NAMETR Nene of a traj ectory file myPresto 4 2 12 UN TRA IO Unit of a trajectory file 60 LI Def aul t DATATYpe Types of trajectory file ENER O Energy traj ectory file Defau t CRA Si ngl e preci si on coordi nate traj ectory file CRB Doubl e preci si on coordi nate traj ectory file 00 0 0 Goordi nate superi nposi ng desi gnati on file Wien calculating an average structure fluctuation of coordinates or RVD O FLUCTUati on YES this desi gnate atons used by superi nposi ng coordi nates to the reference coordi nates NAMEBS Nere of an atomnane desi gnati on file UN TBS IO Lhit of atomnane desi gnati on file O LI Def aul t Cauti ong If UN TBS is Oor a negati ve
17. myPresto 4 2 cosgene ANALYSIS USER MANUAL Version 1 0 Copyright C 2004 2010 National Institute of Advanced Industrial Science and Technology AIST Copyright C 2004 2010 Japan Biological Informatics Consortium JBIC About thi s docunent This document is aseparate volume of myPresto 4 2 USER MANUAL Refer to inyPresto 4 2 USER MANUAL fir the copyright user license agreement authors and cited references ACKNOWLEDGEMENT The research and development of this software was supported by grants from New Energy and Industrial Technology Development Organization NEDO and Ministry of Economy Trade and Industry METD JAPAN This software has been developed by the research project promoted by the late Dr Yoshimasa Kyogoku myPresto 4 2 Contents 1 Qverviewof cosgene ANALYSIS cette eens 5 LL BCU OM es ou ite lineari stg dad pede eae BS Gee ee IE 5 L2 Input data creation 00 teen nee es 5 LAR GOON e e ERES PI where eek ERU cee 5 1 2 l1 lI EXE INPUT Gr OUD eo og ee dal Bh ae Pe exe ed ee RUE 7 12 12 EXE gt AM ysis Group i eee nets 10 2 Sanal e cal cul ations myPresto 4 2 B ank space myPresto 4 2 1 Qveerview of cosgene ANALYSI S Cosgene incl udes the functi on ANALYSIS to anal yze energy trajectory file and coordi nate traj ectory file of MN and MD L1 Execution Ml ecul ar i nf ornati on such as reference coordi nate topol ogy fil e and cal cul ati on condi ti ons et
18. nd force coefficient which formthe walls of CAP This is in addition to the file desi gnati ng atons subj ect to CAP restraint see the chapter on EXE NPUT and desi gnati on of CALCAP CALC There are default values but the user usually desi gnates paraneters other than the force constant FORCAP RADCAP Radi us of CAP restrai nt Wthin this radius the restraint force is 0 and outside of it restraint is deternhned by the potenti al 20 0 D Default FCRCAP Force constant of repulsion potenti al formng the CAP val 150 0 Default FUNCAP Formof repul sion potenti al of the CAP val HARMoni C Quadratic parabola potenti al Def aul t F 0 5 FORCAP R RADCAP 2 R MSS CENTER CF CAIN CAP CENTER Bl Quedratic Bi quadrati c potenti al F 20 25 FCRCAP R 2 RADCAP 2 2 R MSS CENTER CF CAN CAP CENTER myPresto 4 2 18 O O Boundary condi ti ons The boundary cond ti ors wi ch can be used i n nyPresto are a sphere edlipsad or period c boundary cond ti ors acd wththe 6faces of a rectangu ar peral l el epi ped Ari gi dva wi ch provides elastic cdlisionis used in a sphere or d lipad Coman rares are used for sore vari abl es like designati on of the center Wen usi ng peri od c boundary cond ti ons be sure not to forge to desi gate the cycl e PODNE for returning coord nates to the unit cdl In contrast wth CAP restrairt there is no need for a file desi geting apd i
19. ns betveen all atons included in resi dues if the d stance bet veent he resi due centers of nass i s at or bel owthe CUTOF d stance ATOM At ombase cut of f Cal cul ates the interactions between atons if the di stance between the atomcenters of nass is less than the CUICFF di stance RESA Resi due base cutoff Gl cu ates i nteracti on betveen al atons i rcl uded i n resi dues i f the nri nam d stance betveen tw atons of a residue is less than the CUTOF d stance CUILENgth Gutoff length AQ 8 0 Def aul t O EFUNcti on Fornat of relati ve di el ectric functi on i n space CON5 Oelectric function is constant Default D ST O De eri c coretart is proporti ard tothed starcee BA Dstarce DI EVALue Di electric constant of space 1 0 Def aul t myPresto 4 2 14 DO O O O Interaction cal cul ati on swtch Use the fol ow ng sw tch to cal cul ate or not cal cul ate a specific i nteracti on O0 0 001 2 1 3 and 1 4interacti on svi tches AI default val ues are used i n ordi nary MN Mcal cul ati on A thoughit is extrenel y rare this is used onl y when you do not w sh to calculate a certain i nteracti on CALBCNd 1 2 interaction cal cul ati on CALC Cal cul ate Def aul t NOCA c Do not cal cul ate CALANG ef 1 3 interaction cal cul ati on ALC Cal cul ate Def aul t NOCA c Do not cal cul ate CALTCRsi on Torsi on i nteracti on cal cul ati on A C Cal cul ate Def aul t NOCAI C Do not c
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