[ccp4bb] non ccp4 question

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

Previous message:
Subject: Summary: log tools for crystallization conditions
From: "S {- dot -} Thiyagarajan" tyahaa {- at -} YAHOO {- dot -} COM
Date: 2008-10-03

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

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

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

CCP4bb navigation

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

Previous message:
Subject: Summary: log tools for crystallization conditions
From: "S {- dot -} Thiyagarajan" tyahaa {- at -} YAHOO {- dot -} COM
Date: 2008-10-03

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