Re: [AMBER] Best practice for charmm to AMBER conversion with HEME group

From: David A Case <>
Date: Fri, 7 Oct 2016 11:55:27 -0400

On Thu, Oct 06, 2016, Korey M Reid wrote:
> I have been successful in producing psf and crd files in charmm and
> perform minimization of input structure with missing atoms followed
> by solvation then minimization of the new system. The resulting psf
> and crd files were then read into the ParmEd program using the chamber
> command.
> With the output of ParmEd using parmout I am able to minimize my system,
> perform NVT heating over 20ps, I however cannot heat over a longer
> period of time and have my temperature not blow up,

First thing to do is to check the initial energies on the Amber side: if
the coordinates are the same as you used for CHARMM, make sure that the
energies reported by the two programs are (nearly) identical. If so,
run a short energy minimization in both programs: the details won't be
exactly the same, but you should get very similar results on both sides.

Also, use the checkstructure command in cpptraj to look for problems in the
prmtop files. (Also try the checkValidity command in parmed.) These will
identify some (certainly not all) possble problems with the CHARMM->Amber

...good luck...dac

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Received on Fri Oct 07 2016 - 09:00:04 PDT
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