VMD-L Mailing List

From: Benjamin.Haberl_at_physik.uni-muenchen.de
Date: Tue May 17 2016 - 14:48:19 CDT

Dear VMD/NAMD users,

i want to use the MDFF-module of VMD to fit a symmetric protein into a
cryoEM density map. Up to now i used only one symmetry group in my
simulations (like in mdff tutorial). Now i want to add a second
symmetry group but could not get it to work.
The 28mer protein has a 7-folded rotational symmetry with two dimers
per symmetric element und a mirror plane symmetry with 7 dimers per
element(two mirrored rings of 7 dimers). I defined one symmetry
pdb-file per symmetry group with the group in the occupancy column and
the element in the beta column as it is described in the
documentation(http://www.ks.uiuc.edu/Research/namd/2.11/ug/node46.html):
1. symmetryfile(rotation)
ATOM 5 CA PHE ... 1.00 1.00 P1 C
   :
ATOM 24080 CA GLU ... 1.00 7.00 P14 C
   :
ATOM 25611 CA PHE ... 1.00 1.00 P15 C
   :
ATOM 49686 CA GLU ... 1.00 7.00 P28 C

2. symmetryfile(plane)
ATOM 5 CA PHE ... 2.00 1.00 P1 C
   :
ATOM 24080 CA GLU ... 2.00 1.00 P14 C
   :
ATOM 25611 CA PHE ... 2.00 2.00 P15 C
   :
ATOM 49686 CA GLU ... 2.00 2.00 P28 C

In the namd-config file i add:
symmetryRestraints on
symmetryfile siphom_fit-symmetry1.pdb
symmetrykFile siphom_fit-symmetryK1.pdb
symmetryfile siphom_fit-symmetry2.pdb
symmetrykFile siphom_fit-symmetryK2.pdb
symmetryFirstStep 1
symmetryFirstFullstep 200000

Both symmetry files work on their own but together like this the
simulation aborts at the start with the following error:
FATAL ERROR: Every monomer must contain the same number of atoms!
Charm++ fatal error:
FATAL ERROR: Every monomer must contain the same number of atoms!

I also tried to define both groups in one file with one group acting
on the CA-atoms and the second on the other C-atom in the backbone.
The error was the same. It seems NAMD cant distinguish between the two
symmetry groups. What did i do wrong?

Thanks and regards,
Benjamin