Input file
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
* * * * * * * * * * * * * * * * * * * * * * *
saProtocol file:
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
| PDB file | - | inPDB file Default name ./molec.pdb |
| moveRes file | - | moveRes file. User defined moving residue segments Default name ./moveRes.inp. |
Restrain file:
inRestrain file. Default name ./restrAt1.inp # * * * * * * * * * * * * * * * * * * * * * * *
# EXAMPLE
-r inRestrain ( ./restrAt1.inp )
#
User defined harmonically restrained RESidue segments. Atom positions are harmonically restrained around initial positions (coordinates) with harmonic constant defined in the ./MdydPar.inp file
(6x,2i4,a40)
xxxxxxIIIIiiiiAAAAAAAAAA
RESTAT 1 119 PBB CA : ProtBackBone CA restrained
RESTAT 131 175 ALL : ALL atoms restrained
RESTAT 191 216 ALL : ALL atoms
END
#
* * * * * * * * * * * * * * * * * * * * * * * *
| Info file | - OutPut file |
| Result log file | - OutPut file |
| Detail log file | - 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
