[gmx-users] G43a1 RNA dihedrals

Ken ksr at chemistry.umass.edu
Wed Jan 25 03:02:50 CET 2006

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  

[ 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,


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