[gmx-users] CT3 terminal

Mark Abraham mark.abraham at anu.edu.au
Tue Oct 26 03:16:25 CEST 2010

----- Original Message -----
From: Sai Pooja <saipooja at gmail.com>
Date: Tuesday, October 26, 2010 7:26
Subject: [gmx-users] CT3 terminal
To: Discussion list for GROMACS users <gmx-users at gromacs.org>

> Hi, >   > I use pdb2gmx command to convert a pdb file to a .gro and .top file(using CHARMM forcefield). For the C terminus, I use the CT3 option which is NCH3. When I use editconf to get a pdbfile from the .gro file generated, the C=0 and the NCH3  seem to clash in space in pymol.

It looks like Par has borrowed the mechanism for generating two carboxylate oxygens on a C atom (one each cis and trans wrt the third generating atom) for generating one amide nitrogen, and the code doesn't check which of cis and trans is already occupied by the carboxyl oxygen. Please file a Bugzilla so that this gets fixed.

A real solution requires some coding, but you can get a crude work-around by replacing

"1      8       NT       C      CA      N" in share/top/charmm27.ff/aminoacids.c.tdb with
"1      1       NT       C      CA      O"

See chapter 5 for details.

This NT will be too close to carboxyl C, and EM will be needed to fix things.


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