VMD-L Mailing List

From: Paula Mihaljevic-Juric (paula.mihaljevic-juric_at_polytechnique.edu)
Date: Fri Sep 20 2019 - 04:45:38 CDT

Hi!

I am trying to refine a structure using MDFF, but my cross correlation coefficient decreases during the simulation.

I rigid-body docked the structure using Situs and I created the psf using CHARMM.

Than I created the files using:

mol new rib30s_docked.psf
mol addfile rib30s_docked.cor
set sel [atomselect top "all"]
$sel writepdb rib30s_docked.pdb

mdff gridpdb -psf rib30s_docked.psf -pdb rib30s_docked.pdb -o rib30s_doc_grid.pdb

ssrestraints -psf rib30s.psf -pdb rib30s_docked.pdb -o ext_bond.txt -hbonds

mol new rib30s_docked.psf
mol addfile rib30s_docked.pdb

cispeptide restrain -o cis_pep.txt
chirality restrain -o chir.txt

mdff setup -o rib30s -psf rib30s_docked.psf -pdb rib30s_docked.pdb -griddx ../../EMmap/emd_8149.dx -gridpdb rib30s_doc_grid.pdb -extrab { ext_bond.txt cis_pep.txt chir.txt } -gscale 0.3 -gbis on -numsteps 500000

I am not sure it matters, but I am using the experimental map of the same structure. It is a ribosome structure and has 45 MG2+ and 9ZN2+ ions. I also tried to restraint ions in case they are causing the issue.

During the simulation the CC decreases from 0.7 to 0.5-0.2 depending on the length of the simulation.

I am also trying the multi-step approach, but it seems I have the same issue. I applied much higher restraints for proteins, but ended up on the more or less same dead end.

I suppose I am missing something in my script or I am just doing something wrong, but just cannot see it. Perhaps the files I am using or the map is faulty.

What am I missing?

I would appreciate anyones help.

Thanks
Paula