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-- Jonathan Sheehan, Ph.D. Research Assistant Professor, Biochemistry Vanderbilt Univ. Ctr. for Structural Biology 5137 MRB3, 465 21st Avenue S. Nashville, TN 37240-7917 Telephone: (615) 936-2516 http://structbio.vanderbilt.edu/~sheehajh/ On Mon, Oct 5, 2015 at 8:03 AM, Gustavo Seabra <gustavo.seabra.gmail.com> wrote: > 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/amberReceived on Mon Oct 05 2015 - 11:30:04 PDT