Hi. Thanks for the tip. I turned the problem was caused by the PDB file. It seems the water segment was not written properly (starting with residue 1 and then all the way to the last one). After correcting this and then manually editing the new PDB file to change the atom names from TIP3 to SPCE water (i.e. OH2 -> OW ...), I was able to import the PDB to Gromacs. I also passed the option "-renum" to pdb2gmx so the atom numbering was corrected.
Thanks for the tips! Regards, Jernej On Tue, Oct 2, 2012 at 3:54 PM, <gmx-users-requ...@gromacs.org> wrote: > From: "Peter C. Lai" <p...@uab.edu> > Subject: Re: [gmx-users] pdb2gmx with more than 9999 residues > To: Discussion list for GROMACS users <gmx-users@gromacs.org> > Message-ID: <20121002062613.gf94...@cesium.hyperfine.info> > Content-Type: text/plain; charset="us-ascii" > > A pdb file with a resid > 9999 exceeds the proper PDB format. > > You can resolvate a dry lipid bilayer using genbox fine; I don't know what > problem you have with the solvation and minimization using that method, > http://manual.gromacs.org/current/online/genbox.html > > You can also pdb2gmx or editconf the lipids and water separately as you > suggested, then merge the files and run ediconf on the merged file to > renumber the atoms. -- Windows: Re-Boot, Linux: Be-Root. -- 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
