From flavio.seixas from unipar.br Sun Sep 9 18:56:30 2007 From: flavio.seixas from unipar.br (FLAVIO AUGUSTO VICENTE SEIXAS) Date: Mon Sep 10 12:07:31 2007 Subject: [X-plor] Heme bond parameters Message-ID: 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 Pra?a Mascarenhas de Moraes, s/n 87508-210 - UMUARAMA - PR - BRASIL Fone: (+55) 44 36212838 Fax: (+55) 44 36212830 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.bio.net/bionet/mm/x-plor/attachments/20070909/b41d1839/attachment.html From antonello.merlino from unina.it Mon Sep 24 04:29:15 2007 From: antonello.merlino from unina.it (antonello.merlino@unina.it) Date: Mon Sep 24 08:56:21 2007 Subject: [X-plor] xplor installation problem Message-ID: <20070924112915.21v55s3zksgggco4@webmail.unina.it> I am trying to compile XPLOR on a Fedora linux computer and have been able to eliminate all the compiler warnings save one... warning: incompatible implicit declaration of built-in function 'strcpy' ...which is repeated through the compilation of the sources this produces some errrors like Error: Unclassifiable statement in IF-clause at (1) In file drigid.f:1206 END IF 1 Error: Expecting END SUBROUTINE statement at (1) mv: impossibile fare stat di `drigid.o': No such file or directory Can you help me?