> > > 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: [email protected] > > To: [email protected] > > 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: [email protected] > > > To: [email protected] > > > 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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