AMBER Archive (2003)

Subject: Re: delphi with amber 7

From: Nori (okimoto_at_atlas.riken.go.jp)
Date: Fri Jul 11 2003 - 21:15:30 CDT

Dear Dr.Guanglei Cui;
Thank you for your advice.
I added the charge and radius of 2681 to my_amber94_delphi.crg and
my_parse_delphi.siz.
But I faced the following error.
Furthermore, what should I just do?$B!!(Bwhich file shoud I modified?
atmtypenumbers?
Wish you can give me some details.

Best regards.

Guanglei Cui wrote:

> Hi,
> You can find out what atom 2681 is and what radius it should take.
> mm_pbasa couldn't find the radius for this atom. Hope this helps.
>
> On Friday 11 July 2003 14:34, Noriaki Okimoto wrote:
> > Dear all,
> > I would like to do an MM-PBSA calculation with Delphi and amber 7.
> > My protein has some new atom types. So, I modified my_amber94_delphi.crg
> >
> > and my_parse_delphi.siz, but faced the following error;
> >
> > //////////////////////////////////////////
> > =>> Calculating energy / entropy contributions
> > Calc contrib for ./test_com.crd.1
> > Calc MM/GB/SAS
> > Generate PDB
> > Calc PB
> > Run 0
> > Generate PQR
> > No radius found for 2681 XX XX
> > Died at ./mm_pbsa.pl line 1340, <PDB> line 2683.
> > //////////////////////////////////////////
> >
> >
> > Anyone are so kind to help me?
> >
> > Thanks in advance.
> >
> > Nori
>
> --
> Guanglei Cui
> Dept. of Chemistry
> SUNY at Stony Brook
> Stony Brook, NY 11790 

--

                      (o o)
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Noriaki Okimoto
Computational Science Laboratory
Institute of Physical and Chemical Research (RIKEN)
2-1 Hirosawa, Wako-shi,
Saitama, 351-0198,
Japan
tel: +81-48-467-9415
fax: +81-48-467-4078
mail address: okimoto_at_atlas.riken.go.jp

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