Thank you
Krzysztof
Berk Hess wrote:
Hi,
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.
Berk
Date: Tue, 24 Aug 2010 09:21:44 -0500
From: kkucz...@ku.edu
To: gmx-users@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 ?
Regards
Krzysztof
--
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: kkucz...@ku.edu
http://oolung.chem.ku.edu/~kuczera/home.html
<http://oolung.chem.ku.edu/%7Ekuczera/home.html>
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Krzysztof Kuczera
Professor
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: kkucz...@ku.edu
http://oolung.chem.ku.edu/~kuczera/home.html
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