Re: [AMBER] parmed chamber

From: Song-Ho Chong <>
Date: Fri, 22 Jul 2016 21:57:13 +0900


Check RESI TIP3 part of top file downloaded from ACEMD.
If the BOND part is


you should add H1 and H2 at the end, so that

BOND OH2 H1 OH2 H2 H1 H2

Also, you need to be extremely careful in handling par file
downloaded from ACEMD (C22STAR part).
It contains more than one dihedral term of the same
multiplicity (n), which may not be appropriately handled
by the tools you are using.
If you are not sure, you can modify them by yourself
by referring to posts in charmm forum.


2016-07-22 20:58 GMT+09:00 Neha Gandhi <>:

> 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?
> --
> Regards,
> Dr. Neha S. Gandhi,
> Vice Chancellor's Research Fellow,
> Queensland University of Technology,
> 2 George Street, Brisbane, QLD 4000
> Australia
> LinkedIn
> Research Gate
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Received on Fri Jul 22 2016 - 06:00:10 PDT
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