[gmx-users] atom name problem between .pdb and .rtp

[Anton Feenstra]

Paul Barrett wrote:
> I am trying to model 1FIN.pdb which contains two ATP molecules. The
> names of some of the the atoms in the .pdb file are different to those
> in the .rtp file leading to errors, e.g. in .pdb the first ATP phospohor
> atom is called "PG" and in .rtp it is called "APG".
> 
> I have edited the .pdb file to correct these differences but am left
> with a problem: the longest atom names in the .rtp file are 5 characters
> long, e.g.A01PG. In .pdb format atom names are up to 4 characters
> (columns 13-16 according to PDB webpage). When I run gromacs it
> complains that it does not recognise atom A01P. It seems to have
> truncated the 5 character name I typed in to 4 characters, as it should
> for .pdb format.
> 
> How can I fix this? Presumably this happens whenever anyone models ATP?

1) first convert .pdb to .gro; .gro *will* accept 5 character atom names,
    and pdb2gmx will read .gro as well as .pdb
2) hack the .rtp to match your .pdb; Atom names in the .rtp are not refered
    to elsewhere, internally all that matters are atom types.


-- 
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)                                   |
|________|___________________________________________________________|