Re: [ccp4bb] non ccp4 question

- Protein crystallography

Main steps:

- Protein purification
- Crystallisation

Special:

- Programs for crystallography
- X-ray detectors

Basic tutorials:

   - Chemistry
   - Protein
   - Peptide
   - Amino Acids

Xtal community:

- CCP4BB

CCP4bb navigation

CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

Previous message:
Subject: non ccp4 question
From: Jonathan Marvin Caruthers Jonathan {- dot -} Caruthers {- at -} COLORADO {- dot -} EDU
Date: 2008-10-03

Next message:
Subject: refmac and average B factors
From: Engin Ozkan eozkan {- at -} STANFORD {- dot -} EDU
Date: 2008-10-04

Subject: Re: non ccp4 question
From: Juergen Bosch jbosch {- at -} U {- dot -} WASHINGTON {- dot -} EDU
Date: 2008-10-04

Hi Jonathan,

try using the PRODRG Server with your coordinates, or alternatively
run Refmac reading in the cif file for your ligand.

Jürgen

On 3 Oct 2008, at 14:25, Jonathan Marvin Caruthers wrote:

> Sorry, but I've nowhere else to turn, I hope nobody minds. In
> trying to model a nonyl glucoside ligand into my model, I get the
> following errors when trying to run the refine.inp script:
>
>
> %NBUPDA-ERR: missing nonbonded Lennard-Jones parameters %%%%%%%
> ATOM: SEGId=" ", RESId="2077", NAME="C1 ", CHEMical="C_1 "
> %NBUPDA-ERR: missing nonbonded Lennard-Jones parameters %%%%%%%
> ATOM: SEGId=" ", RESId="2077", NAME="C6 ", CHEMical="C_6 "
> %NBUPDA-ERR: missing nonbonded Lennard-Jones parameters %%%%%%%
> ATOM: SEGId=" ", RESId="2077", NAME="C9' ", CHEMical="C_15"
> %NBUPDA-ERR: missing nonbonded Lennard-Jones parameters %%%%%%%
> ATOM: SEGId=" ", RESId="2077", NAME="O2 ", CHEMical="O_17"
> %NBUPDA-ERR: missing nonbonded Lennard-Jones parameters %%%%%%%
> ATOM: SEGId=" ", RESId="2077", NAME="O3 ", CHEMical="O_18"
> %NBUPDA-ERR: missing nonbonded Lennard-Jones parameters %%%%%%%
> ATOM: SEGId=" ", RESId="2077", NAME="O4 ", CHEMical="O_19"
> %NBUPDA-ERR: missing nonbonded Lennard-Jones parameters %%%%%%%
> ATOM: SEGId=" ", RESId="2077", NAME="O5 ", CHEMical="O_20"
> %NBUPDA-ERR: missing nonbonded Lennard-Jones parameters %%%%%%%
> ATOM: SEGId=" ", RESId="2077", NAME="O6 ", CHEMical="O_21"
> %NBUPDA error encountered: program will be aborted.
> (CNS is in mode: SET ABORT=NORMal END)
> *****************************************************
> ABORT mode will terminate program execution.
> *****************************************************
> Program will stop immediately.
>
> as I understand it this has something to do with O renumbering the
> ligand after one fits it and has O write the coordinates out and
> that the new coordinates don't match up to the NONBonded lists in
> the .par file, however, as a test, I get this error AFTER I
> downloaded the file from Hic-Up, attached it to my generate.inp into
> file, ran the script, and then used the output from the generate.inp
> script as input for the refine.inp script - so there was no
> possibility for O to muck things up. Anyway, it's funny in that
> it's only 8 of 21 atoms that seem to exhibit this problem and not
> the whole mess. Does anyone have any ideas?
>
>
> thanks a lot,
>
>
> Jon Caruthers

-
Jürgen Bosch
University of Washington
Dept. of Biochemistry, K-426
1705 NE Pacific Street
Seattle, WA 98195
Box 357742
Phone: +1-206-616-4510
FAX: +1-206-685-7002
Web: http://faculty.washington.edu/jbosch

CCP4bb navigation

CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

Previous message:
Subject: non ccp4 question
From: Jonathan Marvin Caruthers Jonathan {- dot -} Caruthers {- at -} COLORADO {- dot -} EDU
Date: 2008-10-03

Next message:
Subject: refmac and average B factors
From: Engin Ozkan eozkan {- at -} STANFORD {- dot -} EDU
Date: 2008-10-04