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-- Yong Duan, Ph.D, Professor UC Davis Genome Center and Department of Biomedical Engineering University of California at Davis Davis, CA 95616 530-754-7632 On 11/26/11 11:10 AM, "George Tzotzos" <gtzotzos.me.com> wrote: >Just to clarify my earlier message. > >The complex.pdb file that I submitted to tleap did NOT have connect >records. So the error message is perplexing. > >Which leads me to ask the following question. > >If CONNECT records are included in the the submitted pdb file, does this >mean that it is not necessary to issue an explicit bond command? This is >not clear in the Amber 11 manual. > >Thanks in advance for the advice > >George > > >On Nov 26, 2011, at 7:13 PM, George Tzotzos wrote: > >> Hi everybody, >> >> I'm repeating the preparation of topology files for a ligand-receptor >>complex. >> >> The files have been prepared without tleap issuing any untoward >>warnings. >> >> On solvating the system, I got >> >>> saveamberparm COMPLEX 2erb_indole_solv.prmtop 2erb_indole_solv.inpcrd >> Checking Unit. >> Building topology. >> Building atom parameters. >> Building bond parameters. >> Building angle parameters. >> Building proper torsion parameters. >> !FATAL ERROR---------------------------------------- >> !FATAL: In file [unitio.c], line 1788 >> !FATAL: Message: 1-4: cannot add bond 386 874 >> This may be caused by duplicate bond specifications; >> for example, explicit bond commands in addition to PDB conect records. >> ! >> !ABORTING. >> >> I'm rather stuck. Your advice how to overcome this problem would be >>most welcome. >> >> As I mentioned this is a repeat prep. On earlier occasions I didn't get >>anything like this. The only thing that I did differently this time was >>to construct 3 disulfice bonds issuing the commands: >> >> COMPLEX=loadpdb 2erb_indole.pdb >>> bond COMPLEX.26.SG COMPLEX.57.SG >>> bond COMPLEX.53.SG COMPLEX.104.SG >>> bond COMPLEX.95.SG COMPLEX.113.SG >> >> saveamberparm COMPLEX 2erb_indole.prmtop 2erb_indole.inpcrd >> >> and the same for the receptor. >> >> Best regards >> >> George >> >> >> _______________________________________________ >> AMBER mailing list >> AMBER.ambermd.org >> http://lists.ambermd.org/mailman/listinfo/amber > >_______________________________________________ >AMBER mailing list >AMBER.ambermd.org >http://lists.ambermd.org/mailman/listinfo/amber _______________________________________________ AMBER mailing list AMBER.ambermd.org http://lists.ambermd.org/mailman/listinfo/amberReceived on Sat Nov 26 2011 - 13:00:02 PST