why don't u try center command
and u observed in which viewer system as sometimes it appears as an artifact only.
> Hello evrybody,
>
> I justed posted a few hours ago about a problem encountered when
> solvating a protein with a
> sugar-ligand. Sorry, but in my previous post, I was perhaps too fuzzy.
>
> Using the following commands on the first attached PDB file (ADA.pdb):
>
> source leaprc.ff99
> source leaprc.Glycam_06
> x = loadPDB ADA.pdb
> solvateBox x TIP3PBOX 10.0
> addions x Na+ 0
> saveAmberParm x ADA_Solvated.top ADA_Solvated.crd
> savePDB x ADA_Solvated.pdb
>
> creates a weird solvation box that does not surround the solute at all
> as you can see when looking at the second attached file
> (ADA_Solvated.pdb). Would you have any clue of what is (or I did) wrong
> with my setup ?
>
> thank you very much
>
> Eric
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Apr 01 2010 - 02:30:03 PDT
