AMBER Archive (2008)

Subject: Re: AMBER: antechamber and gaff for a homodimer

From: rebeca (
Date: Thu Nov 27 2008 - 07:33:19 CST

Thank you for your answer. I have already done it. But I would like to see
the difference between doing it with one monomer and the total dimer,
because for example, the distribution of the charges is not the same and it
would be affected by the hydrogen bonds formed between both monomers.
Any idea?

Rebeca García Fandiño

On Thu, 27 Nov 2008 12:27:31 +0000, Alan <> wrote:
> Do for just one monomer, the topology parameters are the same for the
> 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 <> 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
>> -----------------------------------------------------------------------
>> The AMBER Mail Reflector
>> To post, send mail to
>> To unsubscribe, send "unsubscribe amber" (in the *body* of the email)
>> to

The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" (in the *body* of the email)