Do for just one monomer, the topology parameters are the same for the other
monomer!
Think your monomer as residue for example. Would you do the parametrisation
for every ALA you find in a protein?
Cheers,
Alan
On Thu, Nov 27, 2008 at 11:12, rebeca <rebeca.mmb.pcb.ub.es> wrote:
> Hello,
> I am trying to get the parameters for an organic molecule forming a dimer
> with itself (by hydrogen bonds). I am using ANTECHAMBER and GAFF. When I
> use one monomer only, there is no problem, everything is OK, but when I try
> to get the parameters of the dimer as a whole molecule I have problems.
>
> What I do is a HF Gaussian calculation and then
>
> antechamber -i gaussian.log -fi gout -o dimer.prepin -fo prepi -c resp -s 2
>
> This gives me a dimer.prepin file, only with errors of the type "Info: the
> atom number exceeds the MAXATOM, reallocate memory automatically", which
> are not relevant, as I have seen in the mailing list.
>
> When I look at the NEWPDB.PDB file I get, I see that only consist in one
> monomer. The second monomer appears filled by ceros in the coordinates and
> the residue number is also 1, instead of two. This is, it is not
> recognized.
>
> Is it not possible to use antechamber and gaff for a molecule consisting in
> two units not-covalently joined?
>
> Thank you very much for your help.
>
> Rebeca García Fandiño
> rebeca.mmb.pcb.ub.es
>
>
>
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--
Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate
Department of Biochemistry, University of Cambridge.
80 Tennis Court Road, Cambridge CB2 1GA, UK.
>>http://www.bio.cam.ac.uk/~awd28<<
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Received on Fri Dec 05 2008 - 17:58:43 PST
