Hi David, Thanks for the quick reply. My apologies for asking you again a silly doubt as, I am doing this all for the first time. It will be of great help if you can tell me how to do such correction manually.
With Thanx, Vivek 2008/8/12 David van der Spoel <[EMAIL PROTECTED]> > vivek sharma wrote: > >> Hello there, >> I am trying to run pdb2gmx on 3bzu.pdb file and got the following error >> >> Opening library file /usr/share/gromacs/top/ >> ffG43b1.rtp >> Opening library file /usr/share/gromacs/top/aminoacids.dat >> Reading 3bzu.pdb... >> WARNING: all CONECT records are ignored >> Read 'CORTICOSTEROID 11-BETA-DEHYDROGENASE ISOZYME 1; 6 BETA-HSD1', 8581 >> atoms >> Opening library file /usr/share/gromacs/top/xlateat.dat >> 26 out of 26 lines of xlateat.dat converted succesfully >> Analyzing pdb file >> >> ------------------------------------------------------- >> Program pdb2gmx, VERSION 3.3.3 >> Source code file: pdb2gmx.c, line: 878 >> >> Fatal error: >> Chain identifier 'A' was used in two non-sequential blocks (residue 1034, >> atom 7961) >> ------------------------------------------------------- >> as I am new to this field. I'm finding it very difficult to find the >> reason and rectify it. >> Any suggestion would be of great help...... >> > This is a limitation in pdb2gmx. It expects the atoms in the chain A to be > in sequence in the pdb file. You can manually sort the pdb file on the chain > identifier. > > >> With Thanx, >> Vivek >> ------------------------------------------------------------------------ >> >> _______________________________________________ >> gmx-users mailing list gmx-users@gromacs.org >> http://www.gromacs.org/mailman/listinfo/gmx-users >> Please search the archive at http://www.gromacs.org/search before >> posting! >> Please don't post (un)subscribe requests to the list. Use the www >> interface or send it to [EMAIL PROTECTED] >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php >> > > > _______________________________________________ > gmx-users mailing list gmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the www interface > or send it to [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php >
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