Hello all,
I've processed an RNA chain in GROMACS 3.2.1 using the G43a1 ff
to .gro and .top files. Upon trying to generate a .tpr file for
genion, grompp returned an series of warnings leading to a fatal
error, eg.:
WARNING 2 [file "rnatest.top", line 605]:
No default Proper Dih. types, using zeroes
looking at the .top file line 605 I find:
[ dihedrals ]
; ai aj ak al funct c0 c1
c2 c3 c4 c5
2 1 4 5 1
1 4 5 6 1 gd_14
Which indicates that GROMACS does not know how to assign the O1P-P-
O5*-C5* proper dihedral in the RNA backbone, as this dihedral is
blank for every nucleotide.
Unfortunately the example .top file in the 3.2 manual has a different
format,
[ dihedrals ]
; ai aj ak al funct phi cp mult
2 1 3 4 1 1.800000e+02 3.347200e+01 2.000000e+00
and a search of the manual for gd_14 (seemed like a good place to
start) returned nothing.
What is the correct dihedral type for these atoms? How can I modify
GROMACS to assign these correctly?
Many thanks,
Ken
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