[gmx-users] Incorrect C-terminal in peptide starting with GLY

Berk Hess gmx3 at hotmail.com
Tue Aug 24 16:48:18 CEST 2010


I fixed it for the next beta release.
If you need it now, change on line 1574 (my latest version) of src/kernel/pdb2gmx.c
cc->r_start to cc->r_end, or get the 4.5 version from git.


Date: Tue, 24 Aug 2010 09:21:44 -0500
From: kkuczera at ku.edu
To: gmx-users at gromacs.org
Subject: [gmx-users] Incorrect C-terminal in peptide starting with GLY

Hi gmx-users
I am trying to set up a simulation of a 16-residue peptide that starts 
with GLY and ends with GLU
(PDB attached) using OPLS-AA/L and gromacs-4.5-beta3. Here is the 
pdb2gmx command
pdb2gmx -inter -ignh -f b-hp41-56.pdb -p peptide.top -o peptide.gro
the ff, water, ionization state selection goes well,
 I get a selection of N-terminals that includes GLY-NH3+ which is fine
but then the selection of C-terminals does not have COO-, but only GLY-COO-
- as a result the C-terminal GLU ends up with incorrect charge and qtot 
is not an integer
Without the '-inter', the system gets GLY-NH3+ and GLY-COO- as well ...
Could someone suggest a fix for this ?
Krzysztof Kuczera
Departments of Chemistry and Molecular Biosciences
The University of Kansas
2010 Malott Hall
Lawrence, KS 66045
Tel: 785-864-5060 Fax: 785-864-5396 email: kkuczera at ku.edu

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