VMD-L Mailing List

From: Ryan McGreevy (ryanmcgreevy_at_ks.uiuc.edu)
Date: Fri Sep 20 2019 - 07:34:34 CDT

Did you create emd_8149.dx using the mdff griddx command, using the
original density as input?

On Fri, Sep 20, 2019, 5:46 AM Paula Mihaljevic-Juric <
paula.mihaljevic-juric_at_polytechnique.edu> wrote:

> 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
>