[gmx-users] G43a1 RNA dihedrals

[Ken Rotondi]

On Jan 25, 2006, at 3:54 AM, David van der Spoel wrote:

> 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)

There is no way to fix this? It seem as though it should be a trivial  
matter of adding a definition to a ff file.

In searching the contributions section of the GROMACS site I find the  
only references to AMBER are in the AMBCONV utility to change AMBER  
topologies and coordinate files to GROMACS .gro and .top files.  
Searching the site for AMBER returns one hit from Berk Hess detailing  
revisions to 3.3 that concerns AMBCONV.  Where is this force field?

Is this a UA ff or and AA ff? I need a UA ff due to the system size. If  
this flavor of AMBER is AA then I cannot use it.

>
>
>> 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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