[gmx-users] (no subject)

Ken Rotondi ksr at chemistry.umass.edu
Tue Mar 21 17:15:48 CET 2006

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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