[gmx-users] Re: Energy Minimization nan && WARNING 1 [file "blah.itp", line 1020]: No default G96Angle types, using zeroes

[David van der Spoel]

Joern Lenz wrote:
> On Wednesday 16 August 2006 16:32, you wrote:
>> dear gromacs users,
>> i am new to gromacs (using version 3.3.1) and trying to simulate an enzyme
>> which is covalently bound to a piece of dna i.e. a tyrosine is connected to
>> the dna backbone establishing a phosphodiester group.
>> but each time i try to start the simulation using the G43a1 forcefield
>> there occurs a warning like
>> WARNING 1 [file "blah.itp", line 1020]:
>> No default G96Angle types, using zeroes
>> or
>> WARNING 39 [file "blah.itp", line 1509]:
>> No default Proper Dih. types, using zeroes
>>
>> i browsed to the mailing list archive and found lots of problems similar to
>> mine but - forgive me -  i am not able to fix my problem with these hints.
>> i know that i have to add these angles and dihedrals in the itp or rtp
>> files. But where exactly and how.
>>
>> one example oif a missing angle is the connection from one nucleeotide to
>> the next in the DNA (O3* - P - O1P).
>> Can anyone tell me how to add the missing lines and where to do that
>> exactly (perhaps with a little example) ???
>> That would be of great help for me. Otherwise I will die unhappy ...
>>
>> Another problem is: where to tell GROMACS that there is a connective bond,
>> angle, dihedral between an aminoacid (the phenolic group of tyrosine) and
>> the DNA backbone ?
>>
>> So if you have any suggestions that could help me, be so kind and try to
>> answer my question.
>> Have a nice day
>> Joe
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first you probably need to use another force field like amber or opls 
since gromos is not very well suited for DNA.

you can define a special bond in the specbond.dat file. copy it to your 
working dir and edit it as appropriate.

-- 
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://folding.bmc.uu.se
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