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
>
>
> _______________________________________________
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> 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
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Received on Mon Oct 05 2015 - 03:30:02 PDT
