[gmx-users] solvent out of box with genbox
Nuri A Temiz
temiz+ at pitt.edu
Sun Feb 12 00:21:25 CET 2006
Hello gmx users
>I am trying to simulate a Zinc-finger domain. I have searched the mailing
>about Zn-ligand interactions and i decided to fix the Zn since i am only
>interested in keeping the fold stable.
>But when i use pdb2gmx, the program automatically protonates the Cys S and
>NE2. I have checked the manual and fixed the His protonation states, but
>could not change the Cys residues. In the manual, the section for Pdb2gmx
>says that the program can be prompted to change Cys residueprotonation state,
>but i did not see the option to do it.
>I must also add that i just started to use Gromacs, so i may be missing
I have sent this email yesterday. I have already tried -cys on pdb2gmx which
actually is not an option. Then i changed my cysteines by hand on topology
file and added constraints on 2 cysteines,2 histidines and Zn, also
renumbered the topology and gro files.
But everytime i use editconf and genbox, most of my solvent is out od the
box. I checked the box visually, the solute (zn-finger peptide) is in the
center but about 3/4 of the solvent is out of the box.
here are the commands i used for editconf and genbox''
editconf -f speptide -o -bt dodecahedron -d 1.5
genbox -cp out -cs -p speptide -o b4em
by the way, i use gromacs 3.2.1
any help would be great
in the md it should not be a problem since i use pbc.
but why do i see the shift in the solvent molecules visually when i use either
vmd or ngmx.
Thank you very much.
N. Alpay Temiz
Department of Computational Biology &
Department of Molecular Genetics and Biochemistry
School of Medicine, University of Pittsburgh
e-mail:temiz at pitt.edu
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