[gmx-users] Adding sphere of molecules

Mahalakshmi S mlakshmis at iitm.ac.in
Mon Aug 8 07:05:52 CEST 2005


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) ?

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 ?

Thank you very much for your attention and help.

Thanks,
Lakshmi



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