[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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