[gmx-users] RE: RE: trjconv problem
Berk Hess
gmx3 at hotmail.com
Tue Jan 19 16:35:12 CET 2010
Hi,
I put in the option to use GMX_MAXRESRENUM=-1 to get the old behavior.
I also fixed a bug with renumbering of multi-residue molecules.
Berk
From: gmx3 at hotmail.com
To: gmx-users at gromacs.org
Subject: RE: [gmx-users] RE: RE: trjconv problem
Date: Tue, 19 Jan 2010 16:20:05 +0100
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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