AMBER Archive (2009)

Subject: Re: [AMBER] RESP using antechamber with Se atom

From: Junmei Wang (junmwang_at_gmail.com)
Date: Thu Nov 05 2009 - 15:39:46 CST

There are several solutions for this problem.

1-the professional solution
   modify the $AMBERHOME/dat/antechamber/APS.DAT file to append one line
describing the APS parameter for Se
   it should like:
   APS Se 34 2 * * 0 * *
* * *

2-the smart solution - If Se in your molecule acts like oxygen
   replace all " Se " with " O " for your gaussian output (sed 's/ Se / O
/g' g03.log > newg03.log)
   then run antechamber as usual
   at last, manually modify the atom names and atom types for Se.

3-the verbose solution
   run step-by-step antechamber commands to solve the problem, need to know
antechamber package very well.

4- the danger solution - may only work for 'simple" molecules
    run antechamber with "-j 5" or "-j 1"

5- the lazy solution
   wait until the next (probably the next next) version of amber package
comes out. We are working on that !!!

The last three solutions are not recommended !

Good luck

Junmei

On Thu, Nov 5, 2009 at 1:21 PM, Donald Keidel <dkeidel_at_scripps.edu> wrote:

> Hi,
>
> I have calculated the electrostatic potential using gaussian 03 for
> SELENOMETHIONINE. When calculating the esp I added to the gaussian input
> file the vdw radius of Se. Gaussian terminated normally and there is charge
> values in the gaussian output for Se.
>
> when I run the following command:
>
> antechamber -fi gout -fo ac -i input_MSE.gout -o input_MSE.ac -c resp
>
> I get the folloowing output:
>
> For atom[7]:Se1, the best APS is not zero, bonds involved by this atom are
> frozen
>
> The frozen atom type can only be 1, 2, 3, 7 (aromatic single), 8 (aromatic
> double)Error: cannot run "/usr/local/amber10/bin/bondtype -j full -i
> ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac" in
> judgebondtype() of antechamber.c properly, exit
>
>
> I have searched the amber mail archive and found emails regarding Fe with a
> similar error, but could not determine how to resolve this.
>
> Is there a way for antechamber to recognize or find the Se information in
> the gaussian output.
>
> Thank you in advance for your help.
>
> Don
>
> --
> "The major difference between a thing that might go wrong and a thing that
> cannot possibly go wrong is that when a thing that cannot possibly go wrong
> goes wrong it usually turns out to be impossible to get at or repair."
> -- One of the laws of computers and programming revealed
>
> Douglas Adams in "Mostly Harmless"
>
> _______________________________________________________________________
>
> Donald J. Keidel, Ph.D.
> Research Associate
> The Scripps Research Institute
> 3377 N. Torrey Pines Court, Suite 100
> La Jolla, CA 92037
> mail code: TPC-26
> phone: (858) 784-2842
> fax: (858) 784-2341
> dkeidel_at_scripps.edu
> webpage: www.biochemistry.ucr.edu/gru/gradstudents/don_keidel/index.htm
>
>
> _______________________________________________
> AMBER mailing list
> AMBER_at_ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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