[gmx-users] Re: Problem with pdb2gmx

[K.A. Feenstra]

Armen H. Poghosyan wrote:
 > Dear K A. Feenstra,
 >
 >    We try to do molecular dynamics simulation of DPPC bilayers. During the topology file creation by means of pdb2gmx we 
encountered the following problem:
 > The numbering of our molecule model isn't corespond to the one defined in ffgmx.rtp.
 > What must we do?
 > Can we switch off all these checkings?

  From what you write I cannot see what could have gone wrong.
Normally, pdb2gmx will re-order atoms to match the order in
the .rtp entries. You would also not want to turn the checks
off, since you need to be sure which atom is which.

If you provide me with more details, I might be able to help
you further.

P.S. we'd appreciate if you direct your questions to the gromacs
mailing list (gmx-users at gromacs.org). You'll have to subscribe
to the list first (you can do that at www.gromacs.org).


-- 
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)                                   |
|________|___________________________________________________________|