Dear gromacs users, I'm doing simulations of small molecules in lipid bilayers. Doing the simulations with a DMPC bilayer works fine for all 4.x versions of gromacs. But when I try to do an energy minimization of a POPC bilayer, grompp gives the following error:
/people/disk2/sarah/gromacs-4.0.3/bin/grompp -f em.mdp -c system.gro -p popcpalc32.top -o test.tpr Ignoring obsolete mdp entry 'cpp' checking input for internal consistency... processing topology... Opening library file /people/disk2/sarah/gromacs-4.0.3/share/top/ffgmxnb.itp Opening library file /people/disk2/sarah/gromacs-4.0.3/share/top/ffgmxbon.itp Opening library file /people/disk2/sarah/gromacs-4.0.3/share/top/ff_dum.itp Generated 1502 of the 2346 non-bonded parameter combinations Generating 1-4 interactions: fudge = 1 Generated 1068 of the 2346 1-4 parameter combinations Opening library file /people/disk2/sarah/gromacs-4.0.3/share/top/flexspc.itp Opening library file /people/disk2/sarah/gromacs-4.0.3/share/top/spc.itp Opening library file /people/disk2/sarah/gromacs-4.0.3/share/top/ions.itp Excluding 3 bonded neighbours molecule type 'PALC' turning all bonds into constraints... Excluding 3 bonded neighbours molecule type 'POPC' turning all bonds into constraints... Excluding 2 bonded neighbours molecule type 'SOL' turning all bonds into constraints... processing coordinates... double-checking input for internal consistency... renumbering atomtypes... converting bonded parameters... ------------------------------------------------------- Program grompp, VERSION 4.0.3 Source code file: convparm.c, line: 68 Fatal error: Value of 'multiplicity' in Proper Dih. is 0, which is smaller than the minimum of 1 ------------------------------------------------------- When looking through the lipid .itp file (popc.itp) I do see dihedrals with multiplicity of 0 (which is not the case in dmpc.itp) - I haven't made it myself but it has been used many times before. When running grompp in version 3.3.3 I get no error message: /people/disk2/sarah/gromacs-3.3.3/bin/grompp -f em.mdp -c system.gro -p popcpalc32.top -o test.tpr creating statusfile for 1 node... Back Off! I just backed up mdout.mdp to ./#mdout.mdp.1# checking input for internal consistency... calling /lib/cpp... processing topology... Generated 1502 of the 2346 non-bonded parameter combinations Generating 1-4 interactions: fudge = 1 Generated 1068 of the 2346 1-4 parameter combinations Excluding 3 bonded neighbours for PALC 32 turning all bonds into constraints... Excluding 3 bonded neighbours for POPC 128 turning all bonds into constraints... Excluding 2 bonded neighbours for SOL 9800 turning all bonds into constraints... processing coordinates... double-checking input for internal consistency... renumbering atomtypes... converting bonded parameters... # ANGLES: 17832 # PDIHS: 5152 # RBDIHS: 2688 # IDIHS: 608 # LJ14: 4288 # CONSTR: 26512 Walking down the molecule graph to make shake-blocks initialising group options... processing index file... Analysing residue names: Opening library file /people/disk2/sarah/gromacs-3.3.3/share/top/aminoacids.dat There are: 9960 OTHER residues There are: 0 PROTEIN residues There are: 0 DNA residues Analysing Other... Making dummy/rest group for T-Coupling containing 36440 elements Making dummy/rest group for Acceleration containing 36440 elements Making dummy/rest group for Freeze containing 36440 elements Making dummy/rest group for Energy Mon. containing 36440 elements Making dummy/rest group for VCM containing 36440 elements Number of degrees of freedom in T-Coupling group rest is 82805.00 Making dummy/rest group for User1 containing 36440 elements Making dummy/rest group for User2 containing 36440 elements Making dummy/rest group for XTC containing 36440 elements Making dummy/rest group for Or. Res. Fit containing 36440 elements Making dummy/rest group for QMMM containing 36440 elements T-Coupling has 1 element(s): rest Energy Mon. has 1 element(s): rest Acceleration has 1 element(s): rest Freeze has 1 element(s): rest User1 has 1 element(s): rest User2 has 1 element(s): rest VCM has 1 element(s): rest XTC has 1 element(s): rest Or. Res. Fit has 1 element(s): rest QMMM has 1 element(s): rest Checking consistency between energy and charge groups... writing run input file... Does anyone have any suggestions? Thank you, Sarah _______________________________________________ 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
