[gmx-users] Adding sphere of molecules
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.
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