Input file. The inProtocol file defines protocol of mdyn calculations. Default file name ./MdynPar.inp . inProtocol file consist of sequense of lines. Line starts from keyWord [and its value]. Example of inProtocol file: #MdynPar.inp for HomologyModel refinement #234567890123456789012345678901234567890!comment $fullProtMD ! #$MovingRes $harmAt1PosRst=0.25 !harmConst (kcal/A^2) $Hread $shake=2 !0/1/2 $zeroRot #$SolvateExWat=4.5 !ExplicitWaterShell 4.5A #$SolvGS $SolvWbrg $SolvGBorn !SolvGBorn #$mdRestart $doMDyn $MDSA !do SimAnnealing $engCalc $engOptim $nOptStep=1 !max N optim steps $aSoftCore=1.0 ! 1.0= standart VDW, < 1.0 -0.0-softCore $initMDTemp=10.00 ! initial temperature in K $bathMDTemp=50.00 ! bath termostat temperature $runMDnstep=2000 ! number mdyn time step to run $mdTimeStep=0.002 ! md time step $NTV=1 ! statistical ensemble type NTV/NEV = 1/0 $nwtra=500 ! write on HD protein structur in pdb format for each nwtra mdstep # END # NOTE that parameter file formatted, i.e. $ sign should be in the firs position of the line No SPACE to assign value after keyword. # Description: parameter file consists of lines starting from the $ simbol and keyWord keyWord can be two types: logical and digital $MovingRes ! logical required special file to define moving RESidues list $harmAt1PosRst=0.25 ! digital NO SPACE to assign value for keyword keyWord switch on a respective modul of program, some keyWord switch on moduls which in turn needs some special User defined file to work properly. KEYWORD DESCRIPTION #234567890123456789012345678901234567890!comment $fullProtMD !defines FULL (i.e. ALL atoms) of the USER molecule will be free to move in energy relaxation or molDyn $MovingRes ! logical keyWord defines that ONLY a defined set of RESidue are free to move this keyWord is coupled with file -mv moveRes in the argument line of the program mdynSB0 default name for moveRes file is ./moveRes.inp #example of ./moveRes.inp #1arb #aaaaaaIIIIiiii # MOVRES 1 10 !line defines first and last resudues of moving segment MOVRES 45 76 MOVRES 115 260 end ************ $harmAt1PosRst=0.25 ! digital keyWord define RESidue segments with 1 atom position harmonic restrants. 0.25 = harmonic restrain Constant K restrEnergy = 0.5*K(r - r0)**2, the reference position r0 = initialXYZinput.pdb - positions from the initial INPut PDB file which defines INItial structure of molecule this keyWord is coupled with file -r inRestrain of the argument line of the program mdynSB05 default name for inRestrain file is ./restrAt1.inp EXample of inRestrain file: #harmonically restrained RESidue segments #xxxxxIIIIiiiiaaAAAA #(6x,2i4,a40) RESTAT 1 63 PBB ! line starts from keyWord RESTAT numbers=first/last residue of segment ! PBB (only protein backbone atoms are restrained, i.e. side chains are free) RESTAT 78 120 ALL ! ALL (all atoms are restrained) end # --------------------------------------------------- $Hread ! defines that all Hydrogens will be read from input molecule structure -c inPDB file otherwise the ALL HYDrogens will be restored by the program mdynSB05 RECOMENDED: at the first run of a protein with unknown (or partially known) Hydrogen atom. start the mdynSB with off $Hread option, i.e. #$Hread ---------------------------------------------------- $shake=2 ! invoke shake subroutine to keep bonds fixed. shake=1 X--Hydr bonds, (shake=2 all bonds) are fixed -------------------------------------------------------------------------------------------------------- $zeroRot ! invoke procedure to stop overal rotation and translation of molecule ---------------------------------------------------- $SolvateExWat=4.5 ! build explicit water solvation shell of 4.5 A around protein molecule ---------------------------------------------------- $SolvGS ! invoke implicit Gaussian Shell solvation model $SolvWbrg ! implicit WaterBridges between polar atoms $SolvGBorn ! implicit Generalized Born model + SAS HydroPhobic solvation --------------------------------------------------- $mdRestart ! restart molDynamics from the last snapshot mdXYZVfin.pdb the file mdXYZVfin.pdb should be copied to the file mdyn inRestart file mdXYZVin.pdb $doMDyn ! do molecular dynamics $MDSA ! do Molecular Dynamical Simulated Annealing ! coupled with file -sa SAprotocol which define protocol of the simulated annealing Example of SAprotocol.inp file #SA protocol #nSAstep 2 #(f10.1,1x,f8.1,1x,3(f6.1,1x) #234567890x12345678x123456x123456x123456 #ntimeMX tempTg SCvdW wfHb128BB wfhB128BS 100000 500.0 0.8 1.0 1.0 100000 100.0 1.0 1.0 1.0 END # ntimeMX - number of md timeStep tempTg - target temperature in K, this temperature will be reach during ntimeMX steps SCvdW - parameter 0 - 1 to defile softness of the van der waals potential. Soft potential modifies Potential Energy Surface decrease a barriers of conformational transitions wfHb128BB, wfhB128BS - scaling factors for BackBone-BackBone and BackBone-SideChain Hydrogen Bond energy #----------------------------------------------------- --------------------------------------------------- * * * * * * * * * * * * * * * * * * * * * * * * -c inPDB file - standart pdb file REMARK: PDB: ATOM 1 N GLY A 1 11.726 -10.369 10.598 ATOM 2 H1 GLY A 1 11.921 -11.015 9.807 ATOM 3 H2 GLY A 1 12.518 -10.395 11.271 ATOM 4 H3 GLY A 1 10.852 -10.663 11.079 ATOM 5 CA GLY A 1 11.567 -9.015 10.090 ATOM 6 HA2 GLY A 1 10.772 -8.977 9.420 ATOM 7 HA3 GLY A 1 12.439 -8.710 9.612 ATOM 8 C GLY A 1 11.280 -8.099 11.303 ATOM 9 O GLY A 1 11.256 -8.584 12.493 ATOM 10 N VAL A 2 11.060 -6.876 11.020 ATOM 11 H VAL A 2 11.066 -6.574 10.025 etc. TER ! CHAIN TERmination ATOM 1302 N GLY A 94 10.957 -15.678 12.832 ATOM 1303 H GLY A 94 10.735 -14.663 12.877 ATOM 1304 CA GLY A 94 10.193 -16.559 11.950 ATOM 1305 HA2 GLY A 94 9.428 -16.004 11.516 ATOM 1306 HA3 GLY A 94 9.784 -17.323 12.525 ATOM 1307 C GLY A 94 11.016 -17.184 10.843 ... etc. TER ! CHAIN TERmination END ! file END * * * * * * * * * * * * * * * * * * * * * * *
PDB file | - | inPDB file Default name ./molec.pdb |
XYZ+Velocity data | - | The XYZ+Velocity file to REStart MolDyn simulation from the last snapshot. |
Position Restrain data | - | File with definition of harmonic positional restraints for user-specified atoms in a molecule. |
Distance Restrain data | - | File with definition of harmonic distance restraints for user-specified pairs of atoms in a molecule. |
Rigidbody data | - | File with definition of harmonic distance restraints for user-specified pairs of atoms in a molecule. |
saProtocol file . User defined protocol for simulated annealing molecular dynamics. Default file name ./Saprotocol.inp Example of SAprotocol.inp file #SA protocol #nSAstep 2 #(f10.1,1x,f8.1,1x,3(f6.1,1x) #234567890x12345678x123456x123456x123456 #ntimeMX tempTg SCvdW wfHb128BB wfhB128BS 100000 500.0 0.8 1.0 1.0 100000 100.0 1.0 1.0 1.0 END # ntimeMX - number of md timeStep tempTg - target temperature in K, this temperature will be reach during ntimeMX steps SCvdW - parameter 0 - 1 to defile softness of the van der waals potential. Soft potential modifies Potential Energy Surface decrease a barriers of conformational transitions wfHb128BB, wfhB128BS - scaling factors for BackBone-BackBone and BackBone-SideChain Hydrogen Bond energy
moveRes file | - | moveRes file. User defined moving residue segments Default name ./moveRes.inp. |
Output:
Result PDB - The final output PDB file with the best prediction. Other output PDB files will be stored in the result folder.
Result PDB - Run output file.
Molecule name - molecule name myMolec. The name will be added to the left of all files generated by the program, i.e. sequence of molecular dynamics trajectory snapshot files myMolec_mdResXXXX.pdb, molecular dynamic trajectory energy file myMolec_engMd.tra, the final result of mdynSB rum file myMolec_mdXYZVfin.pdb