AMBER Archive (2007)

Subject: Re: AMBER:antechamber fails with large molecules

From: Francesco Pietra (chiendarret_at_yahoo.com)
Date: Sun Nov 11 2007 - 05:13:56 CST


I posted my failure to re-compile antechamber for this new respgen.c in Amber
9. Probably I did a mistake in not setting up config.h properly. Wish to know
about successful re-compilations (Linux).

I would also like to know if this re-compilation can also be carried out in
DOCK 6.1 and latest Chimera (both use mopac, unlike Amber 9).

Thanks

francesco pietra

--- Junmei Wang <junmwang_at_yahoo.com> wrote:

> In the latest respgen.c, a parameter, maximum path length has been added. You
> may specify this parameter to, for example 20 for large molecules to get the
> resp input files in second. I believe in 99.99999% cases, setting this
> parameter to 20 should be sufficient.
>
> Attached please find the modified respgen.c. You need to recompile it.
>
> Best
>
> Junmei
>
> ----- Original Message ----
> From: VANIA MARIA AMARO CALISTO <vania.calisto_at_ua.pt>
> To: junmwang_at_yahoo.com
> Sent: Thursday, November 1, 2007 12:58:57 PM
> Subject: AMBER:antechamber fails with large molecules
>
>
> Dear Junmei Wang,
>
> Please find enclosed the .ac file we are using for running
> respgen. What is your opinion about using RESP charges
> with such a big molecule? If your strategy fails I am
> thinking on using AM1BCC charges. What is your opinion?
> I deeply appreciate your help,
>
> Vānia Calisto
>
>
>
>
>
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