AMBER Archive (2006)

Subject: Re: AMBER: Problem using antechamber

From: Gustavo Seabra (gustavo.seabra_at_gmail.com)
Date: Fri Sep 29 2006 - 14:06:34 CDT

Thanks!

I assume I can generate this mol2/ac file using antechamber, starting
fromthe G03 out file?

Gustavo.

On 9/29/06, Junmei Wang <jwang_at_encysive.com> wrote:
>
> Hi, Gustavo,
> In bondtype, Cl must have a valence of 1, this is why it gave a warning
> message. You may first generate a mol2 or ac file (with resp charges) and
> manually modify atom types/bond types if needed, then use prepgen to produce
> a prepin file if prefer to.
>
>
> Good luck
>
> Junmei
>
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>
> -----Original Message-----
> *From:* owner-amber_at_scripps.edu [mailto:owner-amber_at_scripps.edu] *On
> Behalf Of *Gustavo Seabra
> *Sent:* Friday, September 29, 2006 11:19 AM
> *To:* amber_at_scripps.edu
> *Subject:* AMBER: Problem using antechamber
>
> Hi,
>
> I'm trying to use antechamber to generate parameters for ClO4-.
>
> I used the following procedure:
>
> 1. from a pdb file, create a gaussina input using antechamber:
> $ antechamber -i PCL-.pdb -fi pdb -o pcl-.com -fo gcrt -nc -1
>
> 2. Run the gaussian calculation
>
> 3. Use antechamber to generate the prepin file. Here's where I get the
> error:
>
> $ antechamber -i pcl-.log -fi gout -nc -1 -rn pcl- -o pcl-.prepin -fo
> prepi -c resp
>
> Warning: the assigned bond types may be wrong, please :
> (1) double check the structure (the connectivity) and/or
> (2) adjust atom valence penalty parameters in APS.DAT, and/or
> (3) increase MAXVASTATE in define.h and recompile bondtype.C
> (4) increase PSCUTOFF in define.h and recompile bondtype.C
> Be cautious, use a large value of PSCUTOFF (>10) will significantly
> increase the computer time
> Error: cannot run "/scr/arwen_2/seabra/amber10/exe/bondtype -i
> ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac -j full" in
> judgebondtype() of antechamber.c properly, exit
>
> Am I doing something wrong here?
>
>
> Thanks!
>
> Gustavo.
>
> P.S.: I know that the parameters for this ion are available in the Amber
> parameter database. I'm trying to learn here...
>
>

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