>On Thu, 9 Oct 2014 at 3:00 PM, Sahithya S Iyer <sah2...@gmail.com> wrote: >Hello users >I am trying to generate a topology for CHL (chlorophyll a) using oplsaa ff. I >am using topolbuild1_3 as an automated tool suggested in the Protein-Ligand >Tutorial by Justin A. Lemkul to generate topology using oplsaa ff. >I have converted the pdb file of Chl a to mol2 file ( both of the files >attached herein). On running the mol2 file, it gives the following error - >Fatal error. >Source code file: readmol2.c, line: 765 >Atom 3 (CHB) has 2 connections when required to have 3 > >Can you please guide me as to how this error can be rectified ? >Thanks in advance.
The attachment was not passed on. Topolbuild tries to check for consistent chemistry because the rules for selecting atom types will fail if the mol2 atom types are not consistent with the bonding structure given in the mol2 file. The error message means that atom number 3 does not have enough bonds to it for the atom type specified in the mol2 file. This means there is an error in how the mol2 file was generated. There may be more errors in the mol2 file beyond atom 3 because that error was so severe. I usually use either Chimera or Avogadro to save mol2 files, but with these, the type of the guanidino carbon of arginine needs to be changed to C.cat to meet the Sybyl mol2 specifications. Sincerely, -- Bruce D. Ray, Ph.D. Associate Scientist IUPUI Physics Dept. 402 N. Blackford St., Rm. LD-061 Indianapolis, IN 46202-3273 -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.