Dear all, Using topolbuild the *.gro and *.top file for a GPS molecule (C_6H_14O_5Si) were generated. In the GPS molecule there is a --Si(OH)3 group in which the Si and H are indeed the atoms which produce problem in the topol file. The Si and that H are named like below in the [ atom ] section ;
[ atoms ] ; nr type resnr residu atom cgnr charge mass 1 opls_154 1 GPS O 1 0.00000 15.99940 ; 0.0000000 2 H?? 1 GPS H 1 0.00000 1.00800 ; 0.0000000 3 SI 1 GPS Si 1 0.00000 28.08000 ; 0.0000000 4 opls_136 1 GPS C 2 0.00000 12.01100 ; 0.0000000 5 opls_140 1 GPS H 2 0.00000 1.00800 ; 0.0000000 And then the bond and angle sections wherever those two atoms are involved are empty like below; [ bonds ] ; ai aj funct b0 kb 24 23 1 0.10880 284512. ; H- C 4 6 1 0.10900 284512. ; C- H 4 3 ; C- Si 14 13 ; H- O 13 3 ; O- Si 3 1 ; Si- O 3 15 ; Si- O Any suggestion to overcome the problem would be highly appreciated. Best regards, Alex -- 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.