Re: [AMBER] Problem regarding Chamber and psf file

From: Jason Swails <>
Date: Fri, 31 Oct 2014 11:51:40 -0400

On Fri, Oct 31, 2014 at 10:20 AM, Caitlin Scott <> wrote:

> Dear AMBER users,
> I've been using CHARMM-GUI to generate psf and pdb files of my solvated
> and neutralized protein. Previously, psf files were generated in the
> CHARMM format, but recently, CHARMM-GUI changed its psf file format to
> XPLOR. I can still generate the inpcrd and prmtop files, but the job
> crashes during MD.
> When I submit it with AMBER 12 pmemd.cuda, I get the error message:
> Hydrogen atom 2882 appears to have multiple bonds to atoms 2881 and 2883
> which is illegal for SHAKEH.
> According to the psf file, hydrogen atom 2882 is bonded to an oxygen and
> the other hydrogen in same the water molecule. Is this unusual for the
> TIP3 water model?

​No, this is normal. That is how the geometry of the TIP3P water model is

> When I check the md output file, it says:
> Number of triangulated 3-point waters found: 0

​Amber identifies triangulated 3-point water molecules by looking at atom
and residue names. tleap always names water residues WAT and the atom
names within WAT residues as O, H1, and H2. If the names are not what
sander/pmemd expect them to be, triangulated waters will not be identified
and this error will result.

> ​​
> When I was using CHARMM psf files to generate the inpcrd and prmtop files,
> ​​
> I would get this:
> ​​
> Number of triangulated 3-point waters found: 32385
> ​​
> ​​
> Can someone please explain what is a triangulated water, and why are they
> ​​
> missing when the psf is in the XPLOR format?
> ​​

​I don't think this has anything to do with XPLOR vs. CHARMM format, but
rather that CHARMM-GUI gives water residues (and water atoms) different
names than CHARMM itself does?

Look at the "watnam", "owtnm", "hwtnm1", and "hwtnm2" variables (p. 293 of
the Amber 14 manual) -- you can change those variables in the &cntrl
section of your mdin file to get pmemd.cuda to recognize the water naming
scheme for your system.

> ​​
> When I run this job with AMBER 12 sander, there are still no triangulated
> ​​
> waters, but the job doesn't crash.

​My guess is that means that the regular SHAKE algorithm is used (rather
than the fast, analytical SETTLE) algorithm to fix the water geometry (you
can measure some water geometries to make sure that the constraints are
being correctly applied).


Jason M. Swails
Rutgers University
Postdoctoral Researcher
AMBER mailing list
Received on Fri Oct 31 2014 - 09:00:02 PDT
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