van Bemmelen wrote:
Hi guys,
I have a question about the assignment of charge groups at the
N-terminus when applying the GROMOS 53a6 force field. But this may also
be relevant to other force fields.
When I run pdb2gmx (gmx 3.3.1) on a protein (lysozyme 1AKI in this
case), it gives the following N terminus topology:
==========
; nr type resnr residue atom cgnr charge mass
1 NL 1 LYSH N 1 0.129 14.0067
2 H 1 LYSH H1 1 0.248 1.008
3 H 1 LYSH H2 1 0.248 1.008
4 H 1 LYSH H3 1 0.248 1.008
5 CH1 1 LYSH CA 2 0.127 13.019
6 CH2 1 LYSH CB 2 0 14.027
[...]
==========
In this way, cg1 has a total charge of +0.873 and cg2 has a total charge
of +0.127.
Moreover, when I select an NH2 terminus with the -ter option, the
topology becomes:
==========
; nr type resnr residue atom cgnr charge mass
1 NL 1 LYSH N 1 -0.66 14.0067
2 H 1 LYSH H1 1 0.44 1.008
3 H 1 LYSH H2 1 0.44 1.008
4 CH1 1 LYSH CA 2 -0.22 13.019
5 CH2 1 LYSH CB 2 0 14.027
[...]
==========
Now cg1 has a total charge of +0.22 and cg2 exactly the opposite.
Of course this is only a minor detail. But wouldn't it be better and
more consistent if the CA atom would be assigned to cg1 instead of cg2,
in both cases?
Good point. Please submit a bugzilla.
--
David van der Spoel, Ph.D.
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755.
[EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se
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