[gmx-users] G43a1 RNA dihedrals

[Ken Rotondi]

This is an all atom ff. I cannot use it.

Is there no way to fix G43a1 to recognize and correctly label the  
O1P-P- O5*-C5* proper dihedral? Seriously, looking through the .top  
file clearly ~99% of the information is present to run RNA in G43a1,  
everything save this dihedral. It seems a shame to not fix this one  
problem and make this a functional nucleic acid forcefield.

On Jan 25, 2006, at 12:20 PM, leafyoung81-group at yahoo.com wrote:

> Here it is
> http://folding.stanford.edu/ffamber/
>
> Ken Rotondi <ksr at chemistry.umass.edu> 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
>> >  
>> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 
>> +
>> > +
>> >
>> > _______________________________________________
>> > gmx-users mailing list
>> > gmx-users at gromacs.org
>> > http://www.gromacs.org/mailman/listinfo/gmx-users
>> > Please don't post (un)subscribe requests to the list. Use the
>> > www interface or send it to gmx-users-request at gromacs.org.
>>
>> _______________________________________________
>> gmx-users mailing list
>> gmx-users at gromacs.org
>> http://www.gromacs.org/mailman/listinfo/gmx-users
>> Please don't post (un)subscribe requests to the list. Use the
>> www interface or send it to gmx-users-request at gromacs.org.
> _______________________________________________
> gmx-users mailing list
> gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
-------------- next part --------------
A non-text attachment was scrubbed...
Name: not available
Type: text/enriched
Size: 3816 bytes
Desc: not available
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20060125/ea1d8874/attachment.bin>