Ok. Please keep us posted. If it turns out to be a bug, we can search for a
fix.
Gustavo.
Em 05/10/2015 07:26, "Emilio Lence" <guitarro.de.meixente.gmail.com>
escreveu:
> Hi Gustavo
> Thanks for your interest. A corrupted file was the fist suspicion that I
> have, but I'm not so sure that that is the issue here. It happen with
> different files, from different enzymes, different structures, and in all
> the cases the atoms that are misidentified are the 3 Oxygen atoms present
> in the gamma phosphate of the ATP. When I run AM1/d fails because assigned
> to the fist of this Oxygen atoms a Z number of -1. When I copied this files
> to another machine, the one that could be corrupted, it run without
> problems in several different machines, all with Amber12 installed. In my
> local machine with AmberTools15, other different types of enzyme run OK. Un
> fortunately, I have no access to a machine with the Ambertools14 version. I
> will download and install it, and see what happens.
> I believe that there is a problem with the way the Oxygen atoms of the ATP
> are defined, that is no longer recognized by the new versions.
>
>
>
> 2015-10-02 21:51 GMT+02:00 Gustavo Seabra <gustavo.seabra.gmail.com>:
>
> > Hi Emilio,
> >
> > That shouldn’t happen, and it looks more like a case of corrupted file
> > somehow. Can you send me input input files so I can try them?
> >
> > Gustavo Seabra
> >
> >
> >
> > > Em 02/10/2015, à(s) 15:11, Emilio Lence <
> guitarro.de.meixente.gmail.com>
> > escreveu:
> > >
> > > Dear amber users
> > > Recently I installed the AmberTools 15. When I tried to run a DFTB
> > > calculation with sander module, I couldn't. The reason is that do not
> > > recognised some atoms. In my case were 3 O atoms are recognised not as
> > > oxygen but as ^@^@. As a consequence I have an additional atom type (7
> > > instead of 6) with no parameters for it. I tried to copy de O-X.skf
> files
> > > as ^.^.-X.skf, but the sander module do not recognised the new files
> > > (although it ask for then). In previous versions of amber, you can run
> > the
> > > job without problem.
> > > I'm almost sure that I installed all the updates fro ambertools, but
> > right
> > > now I can't access the website of amber to check if there is son update
> > > related with this problem.
> > > Thanks for your kind attention
> > > Have a nice weekend
> > >
> > >
> > > --
> > > Dr. Emilio Lence Quintana
> > > Organic Chemistry Department-CIQUS
> > > University of Santiago de Compostela
> > > 15782 Santiago de Compostela, Spain
> > > _______________________________________________
> > > AMBER mailing list
> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> >
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> Dr. Emilio Lence Quintana
> Organic Chemistry Department-CIQUS
> University of Santiago de Compostela
> 15782 Santiago de Compostela, Spain
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Mon Oct 05 2015 - 06:30:04 PDT
