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

ram bio rmbio861 at gmail.com
Wed Oct 21 15:04:39 CEST 2009

Dear Justin,

Thanks for the suggestion and advice.
As i have used a modelled protein and want to obtain the lowest energy
configuration of the protein by doing dynamics, i want to collect the
structure (coordinates in pdb) representing average of all the
frames/configurations produced in MD and also the lowest energy
configuration structure (coordinates in PDB) produced during the
simulation, which can be used for docking. Please help how to obtain
the average structure as well as the lowest energy configuration



On Wed, Oct 21, 2009 at 6:08 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:
> ram bio wrote:
>> 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
> If you don't see the protein jumping, then what's the problem?  That's the
> point of using trjconv - to correct periodicity.
>> 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.
> It depends on what you want.  If you want to use the structure from the end
> of 1 ns, use editconf.  Using trjconv to convert an .xtc file to a .pdb file
> will generate a (potentially) very large .pdb trajectory with all of the
> frames you saved.  Probably not what you want.  If there is an intermediate
> frame you want to utilize, use trjconv -dump.
>> 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:
> The structure is minimized after energy minimization, which only provides a
> reasonable attempt at generating a starting structure.  Once the dynamics
> begin, the goal is to reach a equilibrium sampling of
> physiologically-relevant configurations.  The structure may or may not
> deviate substantially from the minimized structure (you can gauge that to
> some extent by RMSD).
> Probably the purpose of minimization before docking is simply to correct any
> weird geometry that may be present in the receptor structure
> -Justin
> --
> ========================================
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> ========================================
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