[gmx-users] Adding sphere of molecules

[David]

On Mon, 2005-08-08 at 10:35 +0530, Mahalakshmi S wrote:
> Dear Gromacs users,
> 
> I am sorry for forgetting to change the subject of the email posted 
> earlier to the mailing list. I would like to solvate the 
> X-ray structure of trypsin-BPTI complex by adding a sphere of TIP3P water 
> molecules with a 20ang radius from the O(gamma) of the catalytic Serine 
> 195. I need your help. I have a few questions before you :
> 
> 1) How could I specifically do it (adding a sphere of  water molecules 
> with a 20ang radius from the O(gamma) of the catalytic Serine195) ?
genbox -shell 2 will do something similar (2 nm around the whole
protein)

solvating first using PBC and then running trjorder may do a better job

> 
> 2) I want to neutralize the trypsin-BPTI complex by placing 15 Cl- ions in
> the positions of largest electrostatic potential and counterions need to 
> be fixed in all simulations. How could I place Cl-  ions in the positions 
> of largest electrostatic potential ?
genion is broken at the moment.
> 
> Thank you very much for your attention and help.
> 
> Thanks,
> Lakshmi
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-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,          75124 Uppsala, Sweden
phone:  46 18 471 4205          fax: 46 18 511 755
spoel at xray.bmc.uu.se    spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
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