[gmx-users] pbc whole
carlajamous at gmail.com
Wed Feb 17 10:08:33 CET 2010
I'm still trying to figure out what happened with my ligand.
Meanwhile, I have another question: I can't figure out how to calculate an
average structure in gromacs.
And does g_rmsf calculate the average structure automatically?
On Tue, Feb 16, 2010 at 5:44 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:
> Carla Jamous wrote:
>> Hi Justin,
>> Thank you for your answer but I'm still not getting my ligand to stay in
>> the box.
>> I tried the following(after taking a look at the mailing list archive):
>> trjconv -s a.tpr -f b.xtc -o c.xtc -center -ur compact -pbc mol (centering
>> on "Protein")
>> trjconv -s d.tpr -f c.xtc -o f.xtc -fit rot+trans
>> So please do you have another advise to give me?
> If that's not working, then I wonder if your ligand is still actually bound
> to your protein :) The above sequence always works for me, as long as there
> actually is a complex. You can also try -pbc cluster, but I know that
> algorithm can hang.
>> On Mon, Feb 15, 2010 at 4:32 PM, Justin A. Lemkul <jalemkul at vt.edu<mailto:
>> jalemkul at vt.edu>> wrote:
>> Carla Jamous wrote:
>> Hi everyone,
>> I'm using this command to extract my protein and my ligand from
>> the trajectory.
>> trjconv -f prot_md60ns.xtc -s prot_md50.tpr -fit rot+trans -pbc
>> whole -n prot_wat.ndx -o prot_ligand_60ns.xtc < grps >& outtrj
>> Before, I had a problem with residues of my protein showing at
>> the other end of the box, when I display my .xtc with VMD.
>> the "-pbc whole" fixed it.
>> However, now I have another issue: my ligand is at the other end
>> of the box. So please can anyone tell me what can I do to fix
>> that and get a reasonable RMSD value?
>> You may need several more iterations of trjconv (one rarely does the
>> trick), employing -pbc nojump, -pbc cluster, and/or -center. For
>> protein-ligand complexes, I have often found that the combination of:
>> trjconv -pbc mol -ur compact -center
>> (centering on "Protein")
>> does the trick. And it makes molecules whole, as well :) I think
>> there are also some breakdowns (documented somewhere in the list
>> archive) when applying -fit and -pbc in the same step. I believe it
>> is recommended to fix PBC first, then applying any sort of fitting
>> in a separate, subsequent step.
>> Thank you
>> -- ========================================
>> Justin A. Lemkul
>> Ph.D. Candidate
>> ICTAS Doctoral Scholar
>> MILES-IGERT Trainee
>> Department of Biochemistry
>> Virginia Tech
>> Blacksburg, VA
>> jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
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> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> gmx-users mailing list gmx-users at gromacs.org
> 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 gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
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