[gmx-users] Error in protonating ASP in pdb2gmx.

[K.A. Feenstra]

Gerrit Groenhof wrote:
>>Hi to all,
>>
[...]
 >>
>>"Fatal error: Atom HD1 not found in rtp database in residue ASPH,
>>it looks a bit like HD2"
>>
>>There exist only HD2 in rtp. Why pdb2gmx don't use this one instead? 
> 
> 
> You can just change the OD1 to OD2 and vice versa and name the HD1 HD2
> in the pdb file

It sounds like a bug in the .hdb file.



-- 
Groetjes,

Anton
  ________ ___________________________________________________________
|        | Anton Feenstra                                            |
| .      | Dept. of Pharmacochemistry - Vrije Universiteit Amsterdam |
| |----  | De Boelelaan 1083 - 1081 HV Amsterdam - The Netherlands   |
| |----  | Tel: +31 20 44 47608 - Fax: +31 20 44 47610               |
| ' __   | Feenstra at chem.vu.nl - http://www.chem.vu.nl/afdelingen/FAR|
|  /  \  |-----------------------------------------------------------|
| (    ) | Dept. of Biophysical Chemistry - University of Groningen  |
|  \__/  | Nijenborgh 4 - 9747 AG Groningen - The Netherlands        |
|   __   | Tel +31 50 363 4327 - Fax +31 50 363 4800                 |
|  /  \  | K.A.Feenstra at chem.rug.nl - http://md.chem.rug.nl/~anton   |
| (    ) |-----------------------------------------------------------|
|  \__/  | "If You See Me Getting High, Knock Me Down"               |
|        | (Red Hot Chili Peppers)                                   |
|________|___________________________________________________________|