15 jun 2012 kl. 09.16 skrev Mark Abraham: > On 15/06/2012 5:06 PM, Samuel Flores wrote: >> >> HI Guys, >> >> I'm trying to run a short equilibration of p56 tetramer in water. I issue: >> >> /home/flores/local/gromacs/bin/mdrun -v -deffnm em -c >> /home/flores/projects/antibody-design/13JUN12/352/last.2.em.pdb >> >> The problem is that last.2.em.pdb has four chains, but none have chain ID's! >> The file I start with has chains A,B,C, and D, but gromacs seems to strip >> these and replace them all with " ". >> >> Is there any easy way to prevent the chain ID's from being lost? Or do I >> need to write a script to put them back in? >> > > IIRC there has been list traffic about this in the past, if you search. > Certainly grompp doesn't bother trying to retain chain IDs. editconf allows > you to add chain IDs afterwards, but I have no idea if it lets you do it on a > per-group basis. Another option might be taking the final frame in the > trajectory and using it (-f) and your original .pdb file (-s) as input to > trjconv to write a .pdb file, but I don't know if that works.
It seems that some tools honor the chain IDs while some do not. I think trjconv is one of them, so Mark's suggestion would work in that caase. If not, then a combination of cut -b and paste on your new and old pdb would fix your problem. Normally this is not a problem for simulation, but for quick visualization and inspection it's annoying. Erik > > Mark > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the www interface > or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists ----------------------------------------------- Erik Marklund, PhD Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: +46 18 471 6688 fax: +46 18 511 755 er...@xray.bmc.uu.se http://www2.icm.uu.se/molbio/elflab/index.html
-- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
