[gmx-users] OPLS C-terminal Capping of Glu residue a bug?
mceruso at physbio.mssm.edu
Fri Aug 22 20:48:00 CEST 2003
it was a GLU not a GLY at the C-term
From: gmx-users-admin at gromacs.org [mailto:gmx-users-admin at gromacs.org]On
Behalf Of Erik Lindahl
Sent: Friday, August 22, 2003 2:36 PM
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] OPLS C-terminal Capping of Glu residue a bug?
Thanks, I think we've already fixed this, but I'll check it.
You can change the charge manually in the file top/ffoplsaa-c.tdb.
Don't change the atomtype, though - GLY is special since it doesn't
have any real sidechain.
On Friday, August 22, 2003, at 11:24 AM, Marco Ceruso wrote:
> I was generating the topology for a protein with a Glu residue at the
> C-terminus and I got an absurd total charge of -0.13
> It appears that the charge on the C-alpha atom is the culprit. When
> the protein the Ca of Glu is opls_224B with a charge of 0.14, at the
> C-terminus pdb2gmx labels the Glu as opls_285 with a charge of -0.09.
> Looking at other topologies the last residues has an opls_283 for Ca
> with a
> charge of 0.04, which seems to be the correct charge.
> gmx-users mailing list
> gmx-users at gromacs.org
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
gmx-users mailing list
gmx-users at gromacs.org
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-request at gromacs.org.
More information about the gromacs.org_gmx-users