Thank you Tsjerk, <br>but one more question:<br>if I do the following: g_rmsf -f a.xtc -s b.tpr -o rmsf.xvg -ox average.pdb -n c.ndx<br><br>does gromacs claculate the rmsf after fitting to b.tpr or to average.pdb?<br>& if I want it to calculatefluctuations between the position of<br>
particle i and the time-averaged position of the same particle i, do I have to do:<br><br>g_rmsf -f a.xtc -s average.pdb -o rmsf.xvg?????<br><br>Thank you & sorry to bother. I'm just trying to understand what g_rmsf really does, to help me analyze my results.<br>
<br>Carla<br><br><div class="gmail_quote">On Wed, Feb 17, 2010 at 10:25 AM, Tsjerk Wassenaar <span dir="ltr"><<a href="mailto:tsjerkw@gmail.com">tsjerkw@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Hi Carla,<br>
<br>
Justin's recipe should've worked. As he suggested, maybe the ligand is<br>
not with the protein. You can check by multiplying your system with<br>
genconf:<br>
<br>
genconf -f in.pdb -o out.pdb -nbox 2 2 2<br>
<br>
If the ligand is with the protein, one copy will be located in one of<br>
the copies of the protein.<br>
<br>
g_rmsf does write the average structure, if requested. Use the option -ox<br>
<br>
Cheers,<br>
<br>
Tsjerk<br>
<div><div></div><div class="h5"><br>
On Wed, Feb 17, 2010 at 10:08 AM, Carla Jamous <<a href="mailto:carlajamous@gmail.com">carlajamous@gmail.com</a>> wrote:<br>
> Hi Justin,<br>
> I'm still trying to figure out what happened with my ligand.<br>
> Meanwhile, I have another question: I can't figure out how to calculate an<br>
> average structure in gromacs.<br>
> And does g_rmsf calculate the average structure automatically?<br>
><br>
> Thanks again<br>
> Carla<br>
><br>
> On Tue, Feb 16, 2010 at 5:44 PM, Justin A. Lemkul <<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>> wrote:<br>
>><br>
>><br>
>> Carla Jamous wrote:<br>
>>><br>
>>> Hi Justin,<br>
>>> Thank you for your answer but I'm still not getting my ligand to stay in<br>
>>> the box.<br>
>>><br>
>>> I tried the following(after taking a look at the mailing list archive):<br>
>>><br>
>>> trjconv -s a.tpr -f b.xtc -o c.xtc -center -ur compact -pbc mol<br>
>>> (centering on "Protein")<br>
>>> trjconv -s d.tpr -f c.xtc -o f.xtc -fit rot+trans<br>
>>><br>
>>> So please do you have another advise to give me?<br>
>>><br>
>><br>
>> If that's not working, then I wonder if your ligand is still actually<br>
>> bound to your protein :) The above sequence always works for me, as long as<br>
>> there actually is a complex. You can also try -pbc cluster, but I know that<br>
>> algorithm can hang.<br>
>><br>
>> -Justin<br>
>><br>
>>> Thanks<br>
>>> Carla<br>
>>><br>
>>> On Mon, Feb 15, 2010 at 4:32 PM, Justin A. Lemkul <<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a><br>
>>> <mailto:<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>>> wrote:<br>
>>><br>
>>><br>
>>><br>
>>> Carla Jamous wrote:<br>
>>><br>
>>> Hi everyone,<br>
>>> I'm using this command to extract my protein and my ligand from<br>
>>> the trajectory.<br>
>>><br>
>>> trjconv -f prot_md60ns.xtc -s prot_md50.tpr -fit rot+trans -pbc<br>
>>> whole -n prot_wat.ndx -o prot_ligand_60ns.xtc < grps >& outtrj<br>
>>><br>
>>> Before, I had a problem with residues of my protein showing at<br>
>>> the other end of the box, when I display my .xtc with VMD.<br>
>>> the "-pbc whole" fixed it.<br>
>>><br>
>>> However, now I have another issue: my ligand is at the other end<br>
>>> of the box. So please can anyone tell me what can I do to fix<br>
>>> that and get a reasonable RMSD value?<br>
>>><br>
>>><br>
>>> You may need several more iterations of trjconv (one rarely does the<br>
>>> trick), employing -pbc nojump, -pbc cluster, and/or -center. For<br>
>>> protein-ligand complexes, I have often found that the combination of:<br>
>>><br>
>>> trjconv -pbc mol -ur compact -center<br>
>>><br>
>>> (centering on "Protein")<br>
>>><br>
>>> does the trick. And it makes molecules whole, as well :) I think<br>
>>> there are also some breakdowns (documented somewhere in the list<br>
>>> archive) when applying -fit and -pbc in the same step. I believe it<br>
>>> is recommended to fix PBC first, then applying any sort of fitting<br>
>>> in a separate, subsequent step.<br>
>>><br>
>>> -Justin<br>
>>><br>
>>> Thank you<br>
>>> Carla<br>
>>><br>
>>><br>
>>> -- ========================================<br>
>>><br>
>>> Justin A. Lemkul<br>
>>> Ph.D. Candidate<br>
>>> ICTAS Doctoral Scholar<br>
>>> MILES-IGERT Trainee<br>
>>> Department of Biochemistry<br>
>>> Virginia Tech<br>
>>> Blacksburg, VA<br>
>>> jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> <<a href="http://vt.edu" target="_blank">http://vt.edu</a>> | (540) 231-9080<br>
>>> <a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
>>><br>
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>>><br>
>>><br>
>><br>
>> --<br>
>> ========================================<br>
>><br>
>> Justin A. Lemkul<br>
>> Ph.D. Candidate<br>
>> ICTAS Doctoral Scholar<br>
>> MILES-IGERT Trainee<br>
>> Department of Biochemistry<br>
>> Virginia Tech<br>
>> Blacksburg, VA<br>
>> jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> | (540) 231-9080<br>
>> <a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
>><br>
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<br>
<br>
<br>
</div><font color="#888888">--<br>
Tsjerk A. Wassenaar, Ph.D.<br>
<br>
Computational Chemist<br>
Medicinal Chemist<br>
Neuropharmacologist<br>
</font><div><div></div><div class="h5">--<br>
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