Derek, just following up on this, did building it in Amber tleap work?
On Thu, Aug 17, 2023 at 7:13 PM Derek M Shore via AMBER <amber.ambermd.org>
wrote:
> Hi Dr. Case,
>
> Thanks for the advice. I’ve now simplified the system, such that it only
> contains a 39-residue peptide and a single water. To build this system (as
> input for CHARMM-GUI), I used psfgen to convert the psf to a CHARMM psf,
> and a custom script to format convert the pdb to crd. This is uploaded to
> CHARMM-GUI’s Force Field Converter to generate the parm7 / rst7.
>
> Sadly, it still can’t find the single water (for SETTLE). It’s now trivial
> to verify that the resname is indeed WAT, and the atom names are O, H1, and
> H2. The SOLVENT pointer section also looks okay.
>
> I’ll give tleap a try tomorrow, and we’ll see if this is more successful.
>
> Thanks,
> Derek
>
> Derek M. Shore, Ph.D.
> Lecturer of Physiology and Biophysics
> Scientific Computing Technology Engineer
> Institute for Computational Biomedicine
>
> Weill Cornell Medicine
> Department of Physiology and Biophysics
> 1300 York Avenue, Room LC501A
> New York, NY 10065
> T: 212-746-6386
> des2037.med.cornell.edu<mailto:des2037.med.cornell.edu>
>
> From: David A Case <dacase1.gmail.com>
> Date: Thursday, August 17, 2023 at 9:58 AM
> To: Derek M Shore <des2037.med.cornell.edu>, AMBER Mailing List <
> amber.ambermd.org>
> Subject: [EXTERNAL] Re: [AMBER] Error: Fast 3-point water residue, name
> and bond data incorrect!
> On Wed, Aug 16, 2023, Derek M Shore via AMBER wrote:
> >
> >Yes, the waters are indeed at the end of the system.
>
> Sounds like you will need to start with a very simple protein/water system,
> perhaps created by tleap. Verify that it is find the "fast three-point
> waters". Then try the CHARMM/GUI on the same system. Gradually increase
> the complexity of the system until the fast waters are no longer found.
>
> ...good luck...dac
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Received on Wed Aug 23 2023 - 05:00:02 PDT
