VMD-L Mailing List

From: Patrick Ladam (ladam_at_smbh.smbh.univ-paris13.fr)
Date: Mon Mar 17 2003 - 05:24:31 CST

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 

-- 
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| Patrick LADAM                   |                               |
| Laboratoire CSSB                |     THE BIG BANG THEORY:      |
| UFR SMBH                        |                               |
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| e-mail:                         |                               |
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