Hi 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.
When I look in the G43a1.rtp file I find that there are two listings
for this dihedral:
Courier -O P O5* C5* gd_11
-O P O5* C5* gd_9
With the gd_11 and gd_9 pre-processor codes defined in the .itp file
as:
Courier#define gd_9 0.000 3.14 2
; -OA-P- 0.75
;
#define gd_11 0.000 1.05 3
; -OA-P- 0.25
What do these numbers mean? I cannot make sense based upon the proper
dihedral header in the .itp file
Courier; Dihedral-angle type code
; Force constant
; Phase shift
; Multiplicity
; Example of usage in terms of non-bonded atom types
Could someone who understands this please give me some insight into
how to overcome this problem?
Many Thanks,
Ken