On 03/02/2011 06:42 AM, steinbrt.rci.rutgers.edu wrote:
> Hi,
>
>> does anybody have a script or program that takes a solvated protein
>> structure
>> (as pdb file) and then randomly replaces water molecules by counterions ?
>> Preferentially, it would lead to a neutralized system and would take a
>> concentration as input.
> xleap in amber does something *like* this, but it places ions at
> electrostatically reasonable positions instead of randomly (which might be
> preferable...). Check the addions command.
>
> source leaprc.ff10
> foo = loadpdb<name.pdb>
> addions foo Na+ 5 Cl- 3
> savepdb foo<newname.pdb>
>
> It does read and write pdb files, if they contain only protein and water.
>
> Kind Regards,
>
> Thomas
>
> Dr. Thomas Steinbrecher
> formerly at the
> BioMaps Institute
> Rutgers University
> 610 Taylor Rd.
> Piscataway, NJ 08854
>
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If you want random ion positions after placing them with xleap, you can
use ptraj to do this. See the "randomizeions" command on page 120 of
the AmberTools 1.4 manual.
-Hugh Heldenbrand
Grad Student, University of Minnesota
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Received on Wed Mar 02 2011 - 05:00:05 PST
