[gmx-developers] pdb2gmx

[Anton Feenstra]

Tsjerk Wassenaar wrote:
> Hi Ran,
> 
>> 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.
> 
> Of course that's just a matter of exchanging coordinates. I have a
> script doing that following checking with WHATCHECK. Of course, having
> pdb2gmx dealing with it would have some merits.

Doesn't pdb2gmx check for an (optimal?) H-bonding network for ASP and 
GLU protonation?

Otherwise IMHO the issue is moot, since the group is rotatable, so both 
oxygens are interchangable in the structure (and will swap during 
simulation).


-- 
Groetjes,

Anton
  _____________ _______________________________________________________
|             |                                                       |
|  _   _  ___,| K. Anton Feenstra                                     |
| / \ / \'| | | IBIVU/Bioinformatics - Free University  Amsterdam     |
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