[gmx-users] Solvent_box

[Tsjerk Wassenaar]

Hi Prasenjit,

In addition to the previous comments, note that the default triclinic
box has -angles set to 90 90 90. If you want to have something other
than rectangular, you need to set the angles explicitly. Also, you
issue -d 0.9 and -box 20 10 10. I'm not sure what will happen, but
obviously editconf can't meet both requests at the same time. Either
you set the distance from the solute to the wall or you specify the
vector lengths.

Cheers,

Tsjerk

On 7/12/07, Yang Ye <leafyoung at yahoo.com> wrote:
> Which visualization software you have used?
>
> On 7/12/2007 1:47 PM, pkmukher wrote:
> > Hi,
> >
> >   I am trying to build a triclinic solvent box around
> > two.pdb using the following commands
> >
> > editconf -bt triclinic -f two.pdb -o three.pdb -d 0.9 -box
> > 20 10 10
> > genbox -cp three.pdb -cs spc216.gro -o four.pdb -p two.top
> >
> >
> >
> > However the generated pdb file four.pdb shows a cubic
> > solvation box instead of a triclinic box.Could you please
> > suggest how i should modify the command.Thanks
> >
> >
> >
> > Prasenjit Kumar Mukherjee
> > Graduate Student
> > Department of Medicinal Chemistry
> > School of Pharmacy
> > University of Mississippi
> > USA
> >
> > Cell   - 662 380 0146
> > Office - 662 915 1286
> >
> >
> >
> >
> >
> >
> >
> > _______________________________________________
> > gmx-users mailing list    gmx-users at gromacs.org
> > http://www.gromacs.org/mailman/listinfo/gmx-users
> > Please search the archive at http://www.gromacs.org/search before posting!
> > Please don't post (un)subscribe requests to the list. Use the
> > www interface or send it to gmx-users-request at gromacs.org.
> > Can't post? Read http://www.gromacs.org/mailing_lists/users.php
> >
> >
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>


-- 
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623