[gmx-users] Grompp error in 4.x regarding dihedral multiplicity

[Sarah Witzke]

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