Hi, parameters on AAN are ok I was able to succesfully run a MD of AAN
itself. But using cuda I've tried different systems and the problem with
that glycine is the same! Pmemd itself runs ok but we need cuda! We need
to finish this asap!
2017-02-25 11:33 GMT-03:00 David Case <david.case.rutgers.edu>:
> On Fri, Feb 24, 2017, Alicia Merlino wrote:
>
> > The odd thing is that I was able to succesfully run on cuda the same
> system
> > but without the AAN ligand.
>
> I agree that this is quite odd, since the SHAKE error message appeared to
> refer to atoms in a glycine residue. It clearly seems that checks need to
> be
> made on how the AAN ligand is parameterized. But you might double check
> the
> error message and associated pdb file to see if I was interpreting it
> incorrectly.
>
> ....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 Mon Mar 06 2017 - 21:00:03 PST
