Hi David, thank you for your advice. I ran parmed and the prmtop is ok. I´m
using the same prmtop for minimization and heating but during minimization
SHAKE was turned off. I´ll try to make the heating with ntpr=1 to get more
information. I´m using Amber14 implemented on the Amber package with the
ff14SB force field for the protein.
2017-02-22 17:49 GMT-03:00 David Case <david.case.rutgers.edu>:
> On Wed, Feb 22, 2017, Alicia Merlino wrote:
> >
> > 80: 177 - 178 and 81: 177 - 179
> > Hydrogen atom 177 appears to have multiple bonds to atoms 178 and 179
> which
> > is illegal for SHAKEH.
> > Exiting due to the presence of inconsistent SHAKEH hydrogen clusters.
>
> As Hai suggested, use parmed to look at atoms 177 to 179 (which appear to
> be CA, HA2 and HA3 in a glycine). I admit that this looks like a very
> odd error. Is there any chance that the prmtop file has changed between
> the
> minimization and heating steps? Does the error happen on the very first
> step
> of heating (try to make a very short and simple test case, with ntpr=1,
> to get the most information.) Did you have SHAKE turned on during the
> minimization?
>
> Also, can you say what program you are running, and what version of Amber?
> I'm having trouble finding the location in the code of the errors you
> report above.
>
> ...thx...dac
>
>
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--
Dra. Alicia Merlino
Profesora Adjunta del Laboratorio de Qca. Teórica y Computacional
Instituto de Química Biológica
Facultad de Ciencias, Universidad de la República
Iguá 4225, 11400 Montevideo, Uruguay
Tel: (+598) 2525 2186
Fax: (+598) 2525 0749
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Received on Wed Feb 22 2017 - 15:00:04 PST
