[gmx-users]

[Anton Feenstra]

Rainer Boeckmann wrote:
[...]
>> The following error for Glycerol:
>> Fatal Error:Atom AO1 in residue NDPH 1 not found in rtp entry with 56 
>> atoms
>> while sorting atoms.
>>  
>>
>> What function should I suppose to use to overcome these errors.
>>  
>>
> 
> just rename the atoms according to the respective .rtp entries.

And check if the names correspond to the right .rtp entries; e.g. Ace
may not be available in all forcefields, and NDPH may be called differently.
Also be aware that pdb2gmx has a few built-in rules to rename some
building blocks (like nucleic acid residues and some common alternative
names for amino acid residues).


-- 
Groetjes,

Anton
  _____________ _______________________________________________________
|             |                                                       |
|  _   _  ___,| K. Anton Feenstra                                     |
| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
|(   |   )| | | De Boelelaan 1083 - 1081 HV Amsterdam - Netherlands   |
| \_/ \_/ | | | Tel: +31 20 44 47608 - Fax: +31 20 44 47610           |
|             | Feenstra at chem.vu.nl - www.chem.vu.nl/~feenstra/       |
|             | "If You See Me Getting High, Knock Me Down"           |
|             | (Red Hot Chili Peppers)                               |
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