[gmx-users] [Fwd: help me please]

[Anton Feenstra]

sunzhmd at mail.ustc.edu.cn wrote:
> Hi all,
> 
> I download a pdb file of DEOXYRIBONUCLEIC ACID with many records.Then I
> want to convert it into a gromacs structure file .gro by the
> command
> 
> pdb2gmx -f filename.pdb
> 
> Then a error was encountered which reads
> 
> Residue 'A' not found in residue topology file database

DNA/RNA are not very well implemented and supported. However, many people
have been workin on it recently. Check the archives for the latest
developments, as well as hints for the basic set-up of D/RNA simulations.

> I do not know why. I wonder if you can do me a favor and help me with this
> question.
> 
> By the way, I am a new guy to gromacs. So I wonder if you can tell me
> which records are useful in a officially distributed standard pdb file, as
> far as md simulation is concerned. Are there any differences in format
> between a pdb file that can be handled by pdb2gmx and a officially
> distributed standard pdb file.

Basicall, the only fields pdb2gmx cares about are 'ATOM' and 'HETATM",
the rest is simply ignored. The format is identical to the 'official' one.


-- 
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)                               |
|_____________|_______________________________________________________|