Hi,
> crgmask = "DG9.O6,H1,N2,H21,H22 DC18.N4,H41,H42,H5"
you can't write the crgmask like this. There is a specific format for
writing these masks, Appendix C of the Amber manual has a few examples.
In your case, it would probably look something like this:
(:DG9.O6,H1,N2,H21,H22 | :DC18.N4,H41,H42,H5)
if DG9 and DC18 really are your residue names, which I doubt. You can most
likely just give the residue numbers :9 and :18, *or* the names :DG and
:DC if they are unique (which they normally are not in DNA).
Be careful, since sander will run with any valid chargemask. I think the
output lists all atoms that have their charge stripped, so double-check
these.
Thomas
Dr. Thomas Steinbrecher
formerly at the
BioMaps Institute
Rutgers University
610 Taylor Rd.
Piscataway, NJ 08854
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Received on Tue Feb 07 2012 - 03:00:02 PST
