The Program MDynSB is designed to perform multiple tasks with protein structure:
Program can be executed via the command with argument line
$> MdynSBex -i commandFile -c myPDBfile -o myOUTfile -lp myLoopFile -sa mySAprotocFile
If the argument line does not define some argument file then the default fileName in the current dir will be used by program. Therefore, the user needs to prepare in the CURRENT dir the default name following input files for the MDynSB program (some of them might be omitted):
File names could be set from the command line.
The $ sign (in the first position of a line) defines a KEYWORD.
The # sign defines a comment.
Some keywords should be followed by a numerical or alphabetical value. The following table gives you the list of all keywords allowed. Default values presented in the table are used if the corresponding keyword is not specified.
| Keyword | A short description |
|---|---|
| # | comment |
| $LoopMD | MD for defined LOOPs Note! line starting as # = comment |
| $fullProtMD | MD for full protein |
| $SolvGS | Solvation ON |
| $initMDTemp=10.0 | initial T |
| $bathMDTemp=50.0 | termalBath T |
| $runMDnstep=1000 | max N MD steps |
| $updateR1PL=10 | frequency to Update PAirList |
| $rcutV=8.0 | radius for VDW pairList |
| $rcutC=14.0 | radius for Coulombic pairList |
| $mdTimeStep=0.0010 | MD time step in ps |
| $NTV=1 | ensemble type NTV=1 or NTV=0, |
| $nwtra=200 | frequency to write SNAPshotsb for MD trajectory |
| $molecFile=./molec.pdb | INput pdb proteinFile |
| $loopFile=./loop.inp | LOOP start/end RES Numb |
| $fileSAProt=./SAprotocol.inp | file with SA protocol |
| $xyzMdTra=./xyzMd.tra | xyz trajectory |
| $engMdTra=./engMd.tra | energy trajectory |
| $pdbMdTra=./molMdRes.pdb | pdb trajectory |
| $pdbMdFin=./molMdFin.pdb | pdb Final |
| $MDSA=NO | MD with SIMulatedAnnealing protocol if not NO |
| #END | comment |
Here is an examples of MdynPar.inp file.
To do initial Mdyn slow heat for full protein:
# example-1- do slow heat and make 3000 md time steps # (3 ps - the total simulation time) # $fullProtMD ! MD for full protein $SolvGS ! Solvation ON $initMDTemp=10.0 ! initial T $bathMDTemp=50.0 ! termalBath T $runMDnstep=3000 ! max N MD steps $nwtra=200 ! frequency to write SNAPshotsb for MD trajectory #END
Program will write files in the current directory:
$xyzMdTra=./xyzMd.tra !default - xyz trajectory $engMdTra=./engMd.tra !default energy trajectory $pdbMdTra=./molMdRes.pdb !default pdb trajectory $pdbMdFin=./molMdFin.pdb !default pdb Final
Example 2 of MdynPar.inp
# md for the defined loops $LoopMD $SolvGS !Solvation ON $initMDTemp=10.0 !initial T $bathMDTemp=50.0 !termalBath T $runMDnstep=3000 !max N MD steps $nwtra=200 !frequency to write SNAPshotsb for MD trajectory #END
The loop.inp file has the structure:
#BPTI # tarters # endRes for the Loop #line format = (a6,i4,i4) LOOP1 15 20 LOOP2 40 44 end
Example 3 of MdynPar.inp
# Mdyn of full protein with Simulated Annealing protocol # example-3- do slow heat, make 3000 md time steps # (3 ps - the total simulation time), # make SimulatedAnnealin Mdynamics $fullProtMD !MD for full protein $SolvGS !Solvation ON $initMDTemp=10.0 !initial T $bathMDTemp=50.0 !termalBath T $runMDnstep=3000 !max N MD steps $nwtra=200 !frequency to write SNAPshotsb for MD trajectory $MDSA #END
#SAprotocol #nSAstep 6 ! number of T step #(i8,2x,i8) #2345678**12345678 #ntimeMX tempt T,K 500 10 !number of MD step at the Temperature 500 20 500 30 500 40 500 50 500 50 # end
CPU time is 9-10 min per each 1000 MD step (on athlon 1400 MHz) for protein of about 3000 atoms.
For the most detailed description of the program and its features the reader is referred to MDynSB Manual (MS Word .doc format).