[gmx-users] G43a1 RNA dihedrals

[David van der Spoel]

On Tue, 24 Jan 2006, Ken wrote:

>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.:
>

this is proibably not the answer you want, but try the amber force field 
with gromacs 3.3 (ff available from the contribution section)


>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
>
>

-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
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