[gmx-users] pdb2gmx angles and dihedrals

Elton Carvalho eltonfc at if.usp.br
Wed May 9 15:15:27 CEST 2012

On Tue, May 8, 2012 at 2:04 AM, Mark Abraham <Mark.Abraham at anu.edu.au> wrote:
> Yeah, that .rtp comment looks totally wrong. After looking at the code I
> think:
>    * Column 5: 1 means keep all generated dihedrals,
>    *           0 means permit generated dihedrals to have their parameters
>    *              superseded by ones on the same central bond that have
>    *              fewer hydrogen atoms.
> That's totally different from what the .itp suggests, and does explain your
> observations.
> There seems to be no automatic way to treat the issue that you'd like
> addressed. Feel free to make a feature request on redmine.gromacs.org, but
> it likely won't be addressed until GROMACS 5 (at least).

Thanks, Mark. I think, though, that this case is too specific for a
feature-request. I was just hoping to have an automated tool to do
this boring part.

I guess I'll just postprocess the topology with a script after it's
generated by pdb2gmx.

Good to know that this sparkled some reviewing of the code and the manual =)

> There have been quite a few manual updates already. For example,
> http://jenkins.gromacs.org/job/Manual_Gerrit_4_5/15/ has a link to a current
> PDF manual ("save as" on the PDF link is sometimes necessary). Feedback is
> welcome, but feedback relative to the updated manual is more welcome. :-)

Great. I looked at yesterday's build, right before the reversion and
followed some of the discussion on Gerrit.

I'll submit my suggestions to the redmine site to avoid cluttering the list.

Thanks for the help!
Elton Carvalho
Tel.: +55 11 3091-6985/6922
Dept Física dos Materiais e Mecânica
Instituto de Física
Universidade de São Paulo
P.O. Box 66318 - 05314-970 São Paulo-SP, Brazil

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