[gmx-users] heme group in protein

[Anton Feenstra]

Michel Fodje wrote:
> 
> I've had a few of these problems  especially with atoms or residues that
> have too long names not supported by PDB but present in gromacs
> topologies.
> 
> One thing that works for me is
> 
> editconf -f file.pdb -o file.gro
> 
> Then edit file.gro and change the names to what ever you like, then use
> file.gro as input for pdb2gmx

Alternatively, there is a file called 'xlateat.dat' in your Gromacs
library directory (e.g. <gmx-home>/share/top), which contains a set
of rules for pdb2gmx on how to translate 'pdb' atomnames to 'gromacs'
atom names. The default distribution file reads:
---BEGIN-OF-FILE---
13
ILE      CD1    CD
HOH      O      OW
HOH      OW1    OW
HEME     N_A    NA
HEME     N_B    NB
HEME     N_C    NC
HEME     N_D    ND
protein  O1     O
protein  O2     O
protein  OT     O
protein  OXT    O
protein  O'     O
protein  O''    O
---END-OF-FILE---

You can add your own lines, the first entry on a line is the residue 
name, or 'protein' for any of the recognized amino acids, or '*' or 
'???' for any residue. The next is the 'old' atom name  and the last
is the 'new' atom name (as you could guess). The first line in the
file contains the number of entries, i.e. the number of following 
lines, so bue sure to update it when you add lines.
(NB: you can put your own 'local' copy of xlateat.dat in the local
directory, where you run pdb2gmx, to override the library file.)


-- 
Groetjes,

Anton
 ________ ___________________________________________________________
|        | Anton Feenstra                                            |
| .      | Dept. of Pharmacochemistry - Free University 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   |
| (    ) |-----------------------------------------------------------|
|  \__/  | "Encountered Subspace Anomaly" (Star Trek)                |
|________|___________________________________________________________|