[gmx-users] pdb2gmx

[Anton Feenstra]

herbst at fhi-berlin.mpg.de wrote:

> Hello,
> 
> I tried to create a .top file from a .pdb file for a small molecule (32
> atoms) with pdb2gmx.:
> 
> pdb2gmx -f 81 -o 81 -p 81
> 
> For it is not a standard amino acid, I added the structure of the molecule
> to ffgmx.rtp named 81, but pdb2gmx does not recognize the molecule.  The
> same error appears as before I added the molecule structure to ffgmx.rtp:

In that case, you probably wrote the topology (.rtp format) yourself,
and it would actually be very simple to write your own .top file by hand.
I posted some topology parsing scripts to the list (and/or put them on
the contributions section on the www.gromacs.org) a while ago, which may
be helpful.


-- 
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)                               |
|_____________|_______________________________________________________|