Looks like I've got some work to do. Thanks Mark!
From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Mark Abraham Sent: Thursday, June 03, 2010 4:27 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] pdb2gmx renumbers the residues in my pdb file ----- Original Message ----- From: NG HUI WEN <huiwen...@nottingham.edu.my> Date: Thursday, June 3, 2010 18:08 Subject: [gmx-users] pdb2gmx renumbers the residues in my pdb file To: gmx-users@gromacs.org > Hi, > > I'm a new gromacs user. I have encountered a problem with pdb2gmx where it automatically renumbers the residues in my pdb file. > > For instance, the first residue in my protein F8 has become F1 - this affects all the residues in the protein, something I find rather inconvenient. > > I've been searching the archive for previous posts which might have a solution to this but no luck so far. I might have been wrong. Many thanks for your help. I think you're out of luck. IIRC the facility you want is implemented in the development version, but not yet released. If you re-renumber by hand, then I suspect everything will be fine after that. grompp just needs something whose atom and residue naming and ordering matches the .top... how you produce that doesn't matter to it. Mark << Email has been scanned for viruses by UNMC email management service <http://www.nottingham.edu.my> >> << Email has been scanned for viruses by UNMC email management service >>
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