[gmx-users] reverse transformation with dihedral restraints

francesca vitalini francesca.vitalini11 at gmail.com
Thu Mar 1 11:45:01 CET 2012

I'm trying to do a reverse transformation from coarse grained to all
atom following the MARTINI tutorial and applying it to my system. I
have manually added the dihedral restraint section to my topology and
now, when I try to run the g_fg2cg command I get the following error:

calling cpp...
processing topology...
Generated 165 of the 1596 non-bonded parameter combinations
Cleaning up temporary file gromppGzX0Y4
Program g_fg2cg, VERSION 3.3.1
Source code file: ../kernel/toppush.c, line: 1180

Fatal error:
Incorrect number of parameters - found 7, expected 5 or 5.

"Move Over Hogey Bear" (Urban Dance Squad)

I don't really understand what is going on. I have previously run the
g_dihfix command as suggested in the paper but then I have changed
through a text editor the list of dihedrals to restraint with an
handmade list which contains the omega dihedrals and I have changed
the values of the angles with those obtained through g_angle.

My  command line is g_fg2cg -pcg dynamin_dimer_cg_noWAT.top -pfg
aa_prova_rest.top -c cg.gro -n 0 -o aa_prova_random.gro

Could it be that the error arises from the fact that the dihedral
restraints were calculated from the pdb while the topology was built
through pdb2gmx with the flag -missing? I'm looking at CA C N CA
dihedrals, could any of those atoms be missing?



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