[gmx-developers] pdb2gmx

[hessb at mpip-mainz.mpg.de]

> Hi,
>
> I have to issues regarding pdb2gmx:
>
> 1. With reference to the recent posts regarding "preserving of residue
> numbers": in some proenzymes the residue numbers are with a letter,
> e.g., 48P for residue 48 in the proenzyme (which is different than
> residue 48 although they can be in the same chain). Is this taken into
> account in the new scheme?
>

The old scheme takes this into account and so does the new scheme.
The new code writs the residue insertion codes to top and pdb files,
but all other file formats do not support these insertion codes
and they will therefore be omitted in those formats.

Berk

> 2. How difficult is it to implement the possibility to choose (by the
> user or automatically) which OD atom to protonate for ASPH or GLUH?
> Right now it's not compatible with the FF files, but this is not the
> main issue I guess.
>
> Thanks,
> Ran.
>
> --
> ------------------------------------------------------
> Ran Friedman
> Postdoctoral Fellow
> Computational Structural Biology Group (A. Caflisch)
> Department of Biochemistry
> University of Zurich
> Winterthurerstrasse 190
> CH-8057 Zurich, Switzerland
> Tel. +41-44-6355593
> Email: r.friedman at bioc.unizh.ch
> Skype: ran.friedman
> ------------------------------------------------------
>
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