Thank you Jason, I'll try again with AMBER14.
Regards,
Holly
On Mon, Aug 18, 2014 at 5:14 AM, Jason Swails <jason.swails.gmail.com>
wrote:
> On Sun, 2014-08-17 at 16:42 -0600, Hallel Freedman wrote:
> > Dear AMBER,
> > I am getting an error when trying to run MMGBSA with the idecomp keyword.
> > The error message says:
> >
> > CalcError: /global/software/amber/amber13/bin/sander failed with prmtop
> > ./nw.complex.top!
> > Exiting. All files have been retained.
> >
> > Looking into _MMPBSA_gb_decomp_com.mdin, I have
> >
> > File generated by MMPBSA.py
> > &cntrl
> > ncyc=0, cut=999.0, nsnb=99999, gbsa=2,
> > saltcon=0.15, ntb=0, dec_verbose=0,
> > imin=5, idecomp=1, extdiel=80.0,
> > igb=2, surften=0.0072,
> > /
> > Residues considered as REC
> > RRES 1 500
> > END
> > Residues considered as LIG
> > LRES 501 501
> > END
> > Residues to print
> > RES 1 1 499 499
> > END
> > END
> > bad atom type: o
> >
> >
> > I know that similar errors have been reported, but I still can't figure
> out
> > what's happening here.
>
> This is being hit because the ICOSA surface area parameter for the atom
> type "o" is not programmed into sander. However, as of AmberTools 14
> (as well as some earlier versions, I think), these parameters are
> assigned based on the atomic number rather than the atom type, and I
> would have assumed that the type "o" would have been assigned the atomic
> number of 8 for Oxygen. In this case, oxygen parameters are defined and
> you should not be hitting this error.
>
> The fact that you are suggests to me that you are using an older version
> of AmberTools (i.e., AmberTools 12 or earlier) and that this problem
> would be solved by upgrading to the latest version of AmberTools and
> trying again.
>
> It's always a good idea to tell us what version of Amber you're using
> when asking for help, so we don't have to try and guess ;). You should
> also include all of the bug fixes and updates that have been applied --
> you can type "$AMBERHOME/update_amber --version" to get this
> information. This is always good information to include when reporting
> a problem (even better would be to check the list of updates and see if
> your problem may have already been addressed).
>
> HTH,
> Jason
>
> > I would very much appreciate any suggestions on this.
> > Thanks,
> > Holly
> > _______________________________________________
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> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
>
>
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>
>
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Received on Mon Aug 18 2014 - 10:00:02 PDT
