[gmx-users] ffG43a1.rtp file error

Ken Rotondi ksr at chemistry.umass.edu
Tue Mar 21 17:19:13 CET 2006

(sorry about the blank subject in previous post)

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:

    -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:

#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

; 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,

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