VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Mon Mar 17 2003 - 10:06:11 CST

Hi Patrick,
  I'm forwarding your note to the NAMD developers, hopefully they
can answer your question. (NAMD questions are best sent to namd_at_ks.uiuc.edu
since they don't necessarily read VMD-L regularly...)

Thanks,
  John Stone
  vmd_at_ks.uiuc.edu

On Mon, Mar 17, 2003 at 12:24:31PM +0100, Patrick Ladam wrote:
> Hello All,
>
> I am using NAMD for MD upon a DNA molecule in a water box using
> the charmm FF.It works OK.
> I would like now to use the AMBER forcefield but feel a bit confused
> about what exactly is an AMBER parmfile as I am a total newbie to AMBER.
> I tried simple NAMD runs using a pdb file in correct AMBER format:
> ...
> #
> amber on
> readexclusions no
> ambercoor dna.pdb
> parmfile parm99.dat
> #
> ....
> When I launch NAMD, I have a read error concerning ,the parm99.dat
> file. I did not found precise info upon this in the manual but I think
> the parmfile is the equivalent of the 'structure file' when using the
> charmm FF. So the parm99.dat file I use here might not be the correct
> one expected by NAMD as it is simply a topology file.
> So here is my question:
> How can I generate the correct parmfile starting from my AMBER
> pdb file and the parm99.dat file. psfgen does not handle this
> and I do not have the AMBER program. Is there any available third
> party program to generate AMBER parmfiles I should use?
>
> Thank you all
>
> --
> -----------------------------------------------------------------
> | Patrick LADAM | |
> | Laboratoire CSSB | THE BIG BANG THEORY: |
> | UFR SMBH | |
> | 74 rue Marcel Cachin | In the begining there was |
> | 93017 Bobigny CEDEX | nothing at all. |
> | e-mail: | |
> | ladam_at_smbh.smbh.univ-paris13.fr | Then, it exploded... |
> | Tel: 01 48 38 77 26 / 76 85 | |
> | Fax: 01 48 38 77 77 | |
> ----------------------------------------------------------------- 

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