[X-plor] Heme bond parameters

FLAVIO AUGUSTO VICENTE SEIXAS via x-plor%40net.bio.net (by flavio.seixas from unipar.br)
Sun Sep 9 18:56:30 EST 2007


Hi all,
I'm refining a protein with an heme group. I´m using the topology and
parameter
files from the x-plor library (xplor 3581 for linux rh 9.0), but I'm having
problems to run check.inp
Previous generate and setup_free_r,  runs well without error on *.log file,
but when I was using the check routine, the execution of the program is
terminated with the following message:


POWELL: number of degrees of freedom= 13668

%CODBON-ERR: missing bond parameters %%%%%%%%%%%%%%%%%%%%%%%%%%

bond energy constant missing.

target bond length missing.

ATOM1: SEGId="A ", RESId="142 ", NAME="NA ", CHEMical="NP "

ATOM2: SEGId="A ", RESId="142 ", NAME="C1A ", CHEMical="C "

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

%CODBON-ERR: missing bond parameters %%%%%%%%%%%%%%%%%%%%%%%%%%

bond energy constant missing.

target bond length missing.

ATOM1: SEGId="A ", RESId="142 ", NAME="C1A ", CHEMical="C "

ATOM2: SEGId="A ", RESId="142 ", NAME="C2A ", CHEMical="C "

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

%CODBON-ERR: missing bond parameters %%%%%%%%%%%%%%%%%%%%%%%%%%

bond energy constant missing.

target bond length missing.

ATOM1: SEGId="A ", RESId="142 ", NAME="C2A ", CHEMical="C "

ATOM2: SEGId="A ", RESId="142 ", NAME="C3A ", CHEMical="C "

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%



This message is give for all heme atom bonds exept for iron "FE" bonds.

Please, I appreciate it very much if someone could give me some help.

regards,

-- 
Prof. Dr. Flavio Augusto Vicente Seixas
UNIPAR - Campus Sede / Umuarama
Praça Mascarenhas de Moraes, s/n
87508-210 - UMUARAMA - PR - BRASIL
Fone: (+55) 44 36212838
Fax: (+55) 44 36212830
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