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Topics - cridemichel

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MD simulations / fiber and gromacs
« on: June 18, 2012, 08:57:06 am »
Hi All,
I am a new x3dna user and I would like to use the pdb file generated by fiber
as an input file for gromacs.  I tried to do what follows:

1) I used fiber to generate a file bdna.pdb (see attached 'bdna.pdb' file)

2) pdb2gmx  -f bdna.pdb -o output.gro (selecting interactively: amber99 force field and tip3p water)

but I get the following fatal error:

Fatal error:
Atom P in residue A 1 was not found in rtp entry RA5 with 31 atoms
while sorting atoms.

selecting different force fields or water models do not help,
what's wrong? Any idea?

thank you very much
for your help,

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The Bussemaker Laboratory at the Department of Biological Sciences, Columbia University.