[AMBER] parmed chamber

From: Neha Gandhi <n.gandhiau.gmail.com>
Date: Fri, 22 Jul 2016 21:58:50 +1000

Dear List,

I downloaded top and par files for charmm22* force field available at ACEMD
website. I then used VMD to create psf and pdb files using psfgen, solvate
and ionize plugins of vmd. It seems vmd writes out psf in xplor format.

I then used chamber with nocmap option to convert psf and pdb files to
prmtop and inpcrd. However, I get this error.

 Error: A residue defined as a "fast 3-point water"
        is not defined by a triangle of three bonds.
        Residue 24 contains 2 bonds.

The amber files generated by charmm-gui runs without error.

Does chamber support xplor psf format?

Dr. Neha S. Gandhi,
Vice Chancellor's Research Fellow,
Queensland University of Technology,
2 George Street, Brisbane, QLD 4000
Research Gate
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Received on Fri Jul 22 2016 - 05:00:02 PDT
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