[gmx-developers] pdb2gmx

[Ran Friedman]

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?

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.

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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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