Re: [AMBER] Problem regarding Chamber and psf file

From: Caitlin Scott <>
Date: Fri, 31 Oct 2014 07:20:04 -0700

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

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?

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

Thank you for your help with my previous questions, and I would appreciate
any advice you may have.


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Received on Fri Oct 31 2014 - 07:30:02 PDT
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