[gmx-users] solvent out of box with genbox

[Tsjerk Wassenaar]

Hi ALpay,

For computational reasons, gromacs usually uses the rectangular box
corresponding to the (probably more complex) shape you are using. This is no
problem, since it is always possible to convert a system in one box type
into any other box type, available under pbc. The configuration of the
infinite simulation system is not changed.

Tsjerk

On 2/12/06, Nuri A Temiz <temiz+ at pitt.edu> wrote:
>
> Hello gmx users
> >
> >I am trying to simulate a Zinc-finger domain. I have searched the mailing
> list
> >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
> His
> >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
> >something.
> 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.
> ALpay
> --
> 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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--

Tsjerk A. Wassenaar, M.Sc.
Groningen Biomolecular Sciences and Biotechnology Institute (GBB)
Dept. of Biophysical Chemistry
University of Groningen
Nijenborgh 4
9747AG Groningen, The Netherlands
+31 50 363 4336
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