[gmx-users] Protein Solvent Dynamics - Coordinates for docking

ram bio rmbio861 at gmail.com
Wed Oct 21 14:00:08 CEST 2009

Dear Mark,

Thanks for the advice and suggestions.

I have used trjconv command as in the justin tutorial (trjconv -s
md_0_1.tpr -f md_0_1.xtc -o md_0_1_noPBC.xtc -pbc mol -ur compact),
but when i loaded the md_0_1.gro followed by md_0_1_noPBC.xtc in VMD,
i could not see the protein jumping out of the box on one side. I am
doing something wrong, Please let me know, and  was able to calculate
rmsd plot as per the command: g_rms -s md_0_1.tpr -f md_0_1_noPBC.xtc
-o rmsd.xvg -tu ns

and i want convert the coordinates of the simulated protein in pdb
format, and as I learnt that the coordinates are written in .trr or
.xtc file and i also have a md_0_1.gro file, so can i use editconf -f
md_0_1.gro -o md_0_1.pdb command to convert the coordinates of the
simulated protein into PDB format,is it ok..

or else should i use trjconv -f md_0_1.xtc -o md_0_1.pdb.Please
suggest me the correct script.

Regarding docking when I did solvent simulation on GUI commercial
software, I used to minimize the simulated structure for docking, but
i have no clues learnt in gromacs tutorial ( iam new to gromacs)
regarding the output whether it is  minimized after simulation or not
....the md.mdp file which i used for the production MD is as below:

title		= MD
integrator	= md		
nsteps		= 500000	
dt		= 0.002		
nstxout		= 1000		
nstvout		= 1000		
nstxtcout	= 1000		
nstenergy	= 1000		
nstlog		= 1000		
continuation	= yes		
constraint_algorithm = lincs	
constraints	= all-bonds	
lincs_iter	= 1		
lincs_order	= 4		
ns_type		= grid		
nstlist		= 5		
rlist		= 1.0		
rcoulomb	= 1.0		
rvdw		= 1.0		
coulombtype	= PME		
pme_order	= 4		
fourierspacing	= 0.16		
; Temperature coupling is on
tcoupl		= V-rescale	
tc-grps		= Protein Non-Protein	
tau_t		= 0.1	0.1	
ref_t		= 300 	300	
pcoupl		= Parrinello-Rahman	
pcoupltype	= isotropic	
tau_p		= 2.0		
ref_p		= 1.0		
compressibility = 4.5e-5	
pbc		= xyz		
DispCorr	= EnerPres	
gen_vel		= no	



On Wed, Oct 21, 2009 at 4:42 PM, Mark Abraham <Mark.Abraham at anu.edu.au> wrote:
> ram bio wrote:
>> Dear Gromacs Users,
>> I have performed a protein in solvent simulation for 1 ns, the got the
>> output files as: md_0_1.cpt  md_0_1.edr  md_0_1.gro  md_0_1.log
>> md_0_1.tpr  md_0_1.trr  md_0_1.xtc. I am following Justin Tutorial.
>> Can anybody tell me how to extract the coordinates ? of the simulated
>> protein (file after extraction ?) and is it necessary to minimize the
> It sounds like you should be doing more tutorials to understand GROMACS
> workflows better. What coordinates you produced are in the .trr or .xtc
> files, but what data is there with what frequency is set up in your .mdp
> file, so you need to plan that in advance. trjconv is the tool for
> manipulating those files, for example to extract frames as PDB to use with
> some other software.
>> simulated protein in vacco to use it for further docking studies.
> Maybe. Read the docking literature, or do some tutorials there.
> Mark
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