[gmx-users] Adding sphere of molecules

[Mahalakshmi S]

Hi David,

Thank you very much for your email.
I am actually trying to reproduce  Kollmann's result on BPTI-trypsin. So 
would it give the same results for energy minimization (minimized 
structure) if I do solvation using PBC and then trjorder instead of adding 
a sphere of water molecules with a 20ang radius from oxygen atom(gamma) of 
the serine 195  ?

Regarding genion, do you think it would be fixed soon ? Using genion and
  putting Cl- ions with no random option, would it give the same results for
  energy minimization instead of having Cl- in positions of largest 
electrostatic potential ?

Thanks,
Lakshmi

On Mon, 8 Aug 2005, David wrote:

> 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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