Hello All, I've got a problem with x2top in gromacs 3.3.3. Trying to obtain atopology from ".pdb" structure I do the following: 1. Add >> C C 1 C ; CNT Carbon with one bond >> C C 2 C C ; CNT double bonded Carbon to ffencadv.n2t.
2. Add the following lines [ bondtypes ] ; i j func b0 kb C C 1 0.14210 478900. [ angletypes ] ; i j k func th0 cth C C C 1 120.000 397.480 [ dihedraltypes ] ; i l func q0 cq C C 1 0.000 167.360 to ffgmxbon.itp. 3. Then I execute: x2top -f cnt.pdb -o cnt.top where cnt.pdb is from http://turin.nss.udel.edu/research/tubegenonline.html During the processing I select 7: Encad all-atom force field, using scaled-down vacuum charges The output is Looking whether force field files exist Opening library file /usr/local/gromacs/share/gromacs/top/ffencadv.rtp Opening library file ffencadv.n2t WARNING: all CONECT records are ignored Opening library file ffencadv.n2t There are 0 name to type translations Generating bonds from distances... atom 144 Can not find forcefield for atom C-1 with 0 bonds Can not find forcefield for atom C-2 with 0 bonds Can not find forcefield for atom C-3 with 0 bonds Can not find forcefield for atom C-4 with 0 bonds Can not find forcefield for atom C-5 with 0 bonds Can not find forcefield for atom C-6 with 0 bonds Can not find forcefield for atom C-7 with 0 bonds Can not find forcefield for atom C-8 with 0 bonds Can not find forcefield for atom C-9 with 0 bonds Can not find forcefield for atom C-10 with 0 bonds ............................ ............................ ------------------------------------------------------- Program x2top, VERSION 3.3.3 Source code file: x2top.c, line: 206 Fatal error: Could only find a forcefield type for 0 out of 144 atoms I had not got this error when using version 3.3.1 with this particular task. Why does it consider the carbon has zero bonds...? Any ideas what to do would be gratefully appreciated. Vitaly _______________________________________________ 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
