AMBER Archive (2008)

Subject: AMBER: antechamber and gaff for a homodimer

From: rebeca (rebeca_at_mmb.pcb.ub.es)
Date: Thu Nov 27 2008 - 05:12:23 CST

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_at_mmb.pcb.ub.es

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