Hello! I would like to involve formate molecule (HCOO-)in my dynamics, but I have the problem when I use virtual site (type 3fd)for it.
When I run grompp for single formate molecule, it`s ok. But after solvating in bath of solvent (tip3p) grompp runs with error: Cleaning up constraints and constant bonded interactions with virtual sites Removed 1 Proper Dih.s with virtual sites, 0 left Converted 1 Constraints with virtual sites to connections, 2 left ERROR: Cannot have constraint (5-1) with virtual site (1) ERROR: Cannot have constraint (8-1) with virtual site (1) ERROR: Cannot have constraint (11-1) with virtual site (1) ERROR: Cannot have constraint (14-1) with virtual site (1) .......................................... ERROR: Cannot have constraint (3101-1) with virtual site (1) ERROR: Cannot have constraint (3104-1) with virtual site (1) ------------------------------------------------------- Program grompp, VERSION 3.3.1 Source code file: vsite_parm.c, line: 686 Fatal error: There were 1034 virtual sites involved in constraints ------------------------------------------------------- And 1034 is number of water molecules. In my mdp file the line that corresponds to constraints is "constraints = none". This is my topology: #include "ffoplsaa.itp" [ moleculetype ] ; Name nrexcl FMT 3 [ atoms ] ; nr type resnr residue atom cgnr charge mass 1 opls_279 1 FMT H 1 0.22 0 ; qtot 0.22 2 opls_271 1 FMT C 1 0.58 13.019 ; qtot 0.8 3 opls_272 1 FMT O1 1 -0.9 15.9994 ; qtot -0.1 4 opls_272 1 FMT O2 1 -0.9 15.9994 ; qtot -1 [ bonds ] ; ai aj funct c0 c1 c2 c3 1 2 1 2 3 1 2 4 1 [ angles ] ; ai aj ak funct c0 c1 c2 c3 1 2 3 1 ang_FMT_H_C_O1 1 2 4 1 ang_FMT_H_C_O2 3 2 4 1 ang_FMT_O1_C_O2 [ dihedrals ] ; ai aj ak al funct c0 c1 c2 c3 1 3 2 4 1 improper_O_C_X_Y [ virtual_sites3 ] ; ai aj ak al funct c0 c1 1 2 3 4 2 ; Include water topology #include "tip3p.itp" [ system ] ; Name FMT in water [ molecules ] ; Compound #mols FMT 1 SOL 1034 Could You help me to solve this roblem! Thanks! _____________ Dmitri Nilov _______________________________________________ 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