Re: [AMBER] bad atom type o

From: Jason Swails <>
Date: Mon, 18 Aug 2014 07:14:45 -0400

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
> ./!
> Exiting. All files have been retained.
> Looking into _MMPBSA_gb_decomp_com.mdin, I have
> File generated by
> &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
> Residues considered as LIG
> LRES 501 501
> Residues to print
> RES 1 1 499 499
> 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).


> I would very much appreciate any suggestions on this.
> Thanks,
> Holly
> _______________________________________________
> AMBER mailing list

Jason M. Swails
Rutgers University
Postdoctoral Researcher
AMBER mailing list
Received on Mon Aug 18 2014 - 04:30:02 PDT
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