AMBER Archive (2003)

Subject: Re: delphi with amber 7

From: Guanglei Cui (cuigl_at_morita.chem.sunysb.edu)
Date: Fri Jul 11 2003 - 15:44:09 CDT

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