[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 |
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