Personally I don't think there is a good approach to get good charges (such as HF/6-31G* RESP). AM1BCC may be a good candidate. The problem is that antechamber may not handle such large molecules well. In amber10, I have improved the code a little bit to handle large molecules much better, in a long run I also plan to develop a even simpler, but more reliable charges (compared to am1-bcc) for arbitrary organic molecules. This method will be available in amber11.
Best
Junmei
----- Original Message ----
From: Francesco Pietra <chiendarret.yahoo.com>
To: amber.scripps.edu
Sent: Thursday, November 1, 2007 3:29:26 AM
Subject: Re: AMBER: antechamber fails with large molecules
You may remeber that I tried unsuccessfully to get the partial charges with
Antechamber in Amber9 for a 500-atoms non-repetitive molecule. Prof Case, and
others, suggested, however, that, even if calculated, the partial charges would
be unreliable for such a large residue.
Is the new code intended to solve this question too?
At any event, do you plan to make the new code available? An when? I have
frequently problems of large ligands.
Thanks
francesco pietra
--- Junmei Wang <junmwang.yahoo.com> wrote:
> Could you send me the file? I have modified the respgen.c code a little bit
> to handle large molecules, but it is not in amber9.
>
> Best
>
> Junmei
>
> Dear amber users:
>
> I am trying fit RESP charges with antechamber to a large
> organic molecule (342 atoms) with the command:
>
> antechamber –i biscalix.log –fi gout –o biscalix_resp.mol2
> -fo mol2 –c resp
>
> This fitting process failed with the following errors:
>
> “The number of the path atoms exceeds
> MAXPATHATOMNUM(1900000) for atom[148],extend the size and
> reallocate the memory automatically reallocate memory for
> pathscore[148] failed
> Info: the atom number exceeds the MAXATOM, reallocate
> memory automatically
> Amber 9 RESP
> Unit 5 Error on OPEN: ANTECHAMBER_RESP1.IN
> Error: cannot run "resp -O -i ANTECHAMBER_RESP1.IN -o
> ANTECHAMBER_RESP1.OUT -e ANTECHAMBER.ESP -t qout" in
> resp() of charge.c properly, exit”.
>
> Could someone give me any idea about how to solve this
> type of problems?
>
> Thanks in advance,
> Vânia Calisto
>
>
>
>
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Received on Sun Nov 04 2007 - 06:07:35 PST
