tsjerkw at gmail.com
Thu Jul 12 10:19:13 CEST 2007
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
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
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Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
3584 CH Utrecht
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