[gmx-users] pdb2gmx angles and dihedrals

Elton Carvalho eltonfc at if.usp.br
Mon May 7 21:19:43 CEST 2012

Thank you for your reply, Mark,

On Sat, May 5, 2012 at 7:06 AM, Mark Abraham <Mark.Abraham at anu.edu.au> wrote:
> Fundamentally, pdb2gmx is built for fine-grained force fields. I'd have
> supposed Martini has some kind of builder program other than pdb2gmx, for
> this kind of reason, but I have no idea whether this is true.

It kinda does. Not for polymers just yet. I asked part of the people
involved in this before asking here.

> Setting nrexcl = 1 would exclude such angles and dihedrals, I think, but
> would also exclude generating the normal ones. One option is to do that and
> explicitly define the relevant angles and dihedrals.

nrexcl is already 1, as per MARTINI's defaults and the dihedrals are
built anyway.

> Code comments are in disagreement about column 8. Looking at the code, I
> think the above .rtp comment is how the code works. A specific simple
> counter-example (showing how .rtp contents create .itp contents that seem to
> breach the above description) would be welcome. I'm not sure if there are
> circumstances where impropers are generated automatically, but that could
> possibly explain such an observation.

I prepared a minimal example and, in doing so, I noticed that the
problem is not removing dihedrals sharing a bond with impropers, but
column 5: all_dihedrals, which is said to generate dihedrals involving
ony "heavy" atoms if set to 0.

When set to 1, pdb2gmx generates the dihedrals CA2 CA1 C9 C91 and CA1
C9 C91 C4 for example (see attached figure, remembering this is a
coarse grained model), which are not generated when all_dihedrals is
zero.  Certainly, none of these atoms should be considered "light".

This raises a question about how "heavy" atoms are defined in Gromacs.
I couldn't find it in the PDF manual. Where should I put the
definitions of which atoms are "heavy"?

Also, regardless of the value of RemoveDih, dihedrals like CA2 CA1 C9
C91, that shares the central bond with CA2 CA1 C9 CB1, are kept in the
final topology. So apparently RemoveDih doesn't really exclude proper
dihedrals sharing the central bond.

I prepared a minimal structure and a gmxlib tree which includes the
RTP file for clarification, but it exceeds the attachment limit of the
list, I can send it if itś really necessary

>> Could anyone clarify the role of these extra columns? I think this
>> also hints for a review in this section of the manual.
> True. An update is in progress now.

That's great news!

In the next days I'll send some questions about the manual to help
guiding that effort! ;)

Greetings from a sunny Groningen,
Elton Carvalho
Faculty of mathematics and natural sciences
University of Groningen
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