[gmx-users] RE: RE: trjconv problem

Berk Hess gmx3 at hotmail.com
Tue Jan 19 16:20:05 CET 2010


Hi,

Well, the whole point for this change was that people wanted the original residue numbers,
which in most cases will mean that different subunits will start counting from residue number 1.
The different subunits can be recognized from their chain identifier.

If you want the old numbering, you should set the env.var. GMX_MAXRESRENUM to at least
the largest number of residues in a single molecule.
I can add that the value -1 does the same thing.

Berk

Date: Tue, 19 Jan 2010 13:12:45 -0200
From: stefhoor at gmail.com
To: gmx-users at gromacs.org
Subject: [gmx-users] RE: RE: trjconv problem

Hello, thank you a lot for fixing this in trjconv, but now there is another problem, but perhaps this is simpler to solve. Since my system is formed of a protein dimer in a DPPC membrane, trjconv has renumbered my protein residues starting from one for every new chain. What I mean is: for chain A, protein starts with residue 1 and ends at residue 30, but for chain B, instead of continuing from residue 31 until residue 60 and than continue to residue 61 of DPPC etc, the numbering starts over. So Chain A is numbered from 1 to 30, then Chain B also from 1 to 30 and then DPPC starts at residue 31.....etc. The main problem is that I have a few scripts that analyse my structure files extracted from my trajectory and they rely on the sequential numbering of the residues.

Is there a way to make the numbering go back to the original format?
Thanks






Hi,



I fixed the bug.



But note that this is about residue numbers, not molecules.

The pdb format can not store molecule numbers.

The pdb format is very inconvenient, but unfortunately it is the most used format.



Berk



Date: Mon, 18 Jan 2010 16:51:19 -0200

From: stefhoor at gmail.com

To: gmx-users at gromacs.org

Subject: [gmx-users] RE: trjconv problem















Hi,







It is not a pdb2gmx feature, but a global one.



pdb2gmx is only affected in the sense that it retains the residue numbers from the input pdb.



I assume those will be different for most lipid pdb files (if you use pdb2gmx for those).



This renumbering is done by any program that needs to output or select global residue numbers.



Currently this is switchable with the env.var. I mentioned.



If you put this env.var. in your GMXRC, you can get things how you want them.



Adding an option to all programs is not a good idea.







But I am open for any suggestions on this issue.







There is something I don't get though.



In the problematic output the lipids can not be one single residue, but should be two or more residues.







Berk







> Date: Mon, 18 Jan 2010 10:31:19 -0500



> From: jalemkul at vt.edu



> To: gmx-users at gromacs.org



> Subject: Re: [gmx-users] trjconv problem



>



>



> Could renumbering be a switchable feature?  For instance, pdb2gmx -[no]renumber,



> with "no" being default?  Otherwise, could you provide an example of how to



> properly use the environment variable you posted, since this would seem to



> affect all of us in the membrane protein world quite distinctly (i.e., a



> singly-numbered lipid, as reported, kills many of the programs we have written



> for lipid analysis).



>



> -Justin



>



> Berk Hess wrote:



> > Hi,



> >



> > This is a feature.



> > For a long time users have been complaining that pdb2gmx renumbers the



> > residues in a protein.



> > I have now changed this such that the residue numbers in the pdb are



> > retained.



> > But for for instance solvent you would not like to have this behavior.



> > So I decided to keep numbering single-residue molecules.



> > If you also want you lipids to continue numbering, you'll have to set



> > the env.var. GMX_MAXRESRENUM



> > to the number of residues in a lipid.



> >



> > Berk



> >



> > ------------------------------------------------------------------------



> > Date: Mon, 18 Jan 2010 13:05:42 -0200



> > From: stefhoor at gmail.com



> > To: gmx-users at gromacs.org



> > Subject: [gmx-users] trjconv problem



> >



> > I am trying to use trjconv to extract frames from my protein/membrane



> > system in order to analyse with gdmat. Before using git's latest gromacs



> > version, everything worked just fine. But now, every coordinate file



> > trjconv gives me has the DPPC lipid molecules without numbering. It is



> > like if my membrane was formed of a single DPPC (huge) residue. So



> > instead of generating DPPC residue 1, 2, 3, 4 ....etc, trjconv gives me



> > DPPC residue 1 with 5000 atoms.



> > Some light on the matter would be great.



> > Thanks



> >



I thank you all for the contributions, but the problem is that the command "trjconv" is making funny things and not pdb2gmx. My residues are all numbered correctly. Even my coordinate.gro file that is generated at the end of the simulation has the correct numbering. The problem is specifically with "trjconv".




The output from trjconv comes out like this:

"...

66ASN       O  671   3.212   3.554   5.248

66ASN      HO  672   3.258   3.625   5.302

 1DPP     C33  673   0.623   5.221   1.344

 1DPP     C34  674   0.461   5.360   1.434



 1DPP     C35  675   0.697   5.438   1.420

 1DPP       N  676   0.604   5.327   1.444

 1DPP     C32  677   0.607   5.278   1.583

 1DPP     C31  678   0.722   5.193   1.637

 1DPP     O32  679   0.860   5.229   1.645



 1DPP       P  680   0.954   5.102   1.677

 1DPP     O33  681   0.882   4.986   1.620

 1DPP     O34  682   1.094   5.137   1.647

 1DPP     O31  683   0.929   5.088   1.836

 1DPP      C3  684   1.003   5.184   1.912



 1DPP      C2  685   0.946   5.209   2.052

 1DPP     O21  686   0.988   5.332   2.111

 1DPP     C21  687   0.939   5.454   2.087

 1DPP     O22  688   0.893   5.479   1.976

 1DPP     C22  689   0.952   5.554   2.195



 1DPP     C23  690   1.086   5.626   2.185

 1DPP     C24  691   1.132  -0.046   2.310

 1DPP     C25  692   1.029   0.049   2.372

 1DPP     C26  693   1.080   0.108   2.504

 1DPP     C27  694   1.100   0.015   2.624



 1DPP     C28  695   1.147   0.089   2.750

 1DPP     C29  696   1.047   0.189   2.809

 1DPP    C210  697   1.127   0.248   2.925

 1DPP    C211  698   1.046   0.363   2.985

 1DPP    C212  699   1.127   0.411   3.105



 1DPP    C213  700   1.093   0.323   3.226

 1DPP    C214  701   1.141   0.402   3.348

 1DPP    C215  702   1.107   0.339   3.483

 1DPP    C216  703   1.135   0.428   3.604

 1DPP      C1  704   0.997   5.089   2.132



 1DPP     O11  705   0.921   5.069   2.251

 1DPP     C11  706   0.969   4.974   2.332

 1DPP     O12  707   1.070   4.914   2.295

 1DPP     C12  708   0.886   4.938   2.449

 1DPP     C13  709   0.889   4.790   2.488



 1DPP     C14  710   0.996   4.756   2.592

 1DPP     C15  711   0.985   4.603   2.597

 1DPP     C16  712   1.098   4.556   2.689

 1DPP     C17  713   1.061   4.414   2.730

 1DPP     C18  714   1.174   4.351   2.813



 1DPP     C19  715   1.189   4.364   2.965

 1DPP    C110  716   1.330   4.335   3.017

 1DPP    C111  717   1.367   4.338   3.165

 1DPP    C112  718   1.514   4.304   3.191

 1DPP    C113  719   1.542   4.329   3.339



 1DPP    C114  720   1.691   4.329   3.372

 1DPP    C115  721   1.711   4.346   3.523

 1DPP    C116  722   1.861   4.344   3.549

 1DPP     C33  723   1.394   3.827   1.098

 1DPP     C34  724   1.402   3.868   1.324



 1DPP     C35  725   1.337   3.651   1.249

 1DPP       N  726   1.324   3.795   1.223

 1DPP     C32  727   1.185   3.841   1.213

 1DPP     C31  728   1.074   3.797   1.309

 1DPP     O32  729   1.100   3.828   1.446



 1DPP       P  730   1.029   3.739   1.561

 1DPP     O33  731   0.892   3.693   1.529

 1DPP     O34  732   1.132   3.642   1.606

 1DPP     O31  733   1.020   3.846   1.680

 1DPP      C3  734   1.118   3.824   1.782



 1DPP      C2  735   1.123   3.924   1.898

 1DPP     O21  736   1.254   3.939   1.955

 1DPP     C21  737   1.326   4.049   1.942...."



You see that starting from the second nitrogen atom of my DPPC molecules, the residue number should be 68 and not 2. So this is what trjconv is actually giving me. It is renumbering the solvent molecules but it is not recognising different DPPC molecules. Instead it is writing my DPPC membrane as one single huge molecule.




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