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 Thanks, Ram On Wed, Oct 21, 2009 at 4:42 PM, Mark Abraham <[email protected]> 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 > _______________________________________________ > gmx-users mailing list [email protected] > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the www interface > or send it to [email protected]. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > _______________________________________________ gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [email protected]. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
