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

David van der Spoel spoel at xray.bmc.uu.se
Thu Aug 17 13:15:12 CEST 2006

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 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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