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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