I have a paper under review with an algorithm that does this. It
automatically places water molecules in ideal locations within the protein
(it accurately predicts coordinating water molecules). It is necessary to
first run rism.snglpnt on the system to do so though. Please see
http://sites.google.com/site/dansindhikara/Home/software/placement
There is a link to the software as well as to a tutorial for how to do it
in AMBER.
Please let me know if you have any questions.
-Dan
On Sun, Jan 1, 2012 at 12:35 AM, Sudarshan Debnath <
suarshandebnath.ku.rediffmail.com> wrote:
> Dear Sir/Madam,
>
>
>
> I am a user of AMBER 11. I want to simulate a nucleic acid system. I use
> TIP3P water model to solvate the system. This method adds water molecules
> at the surrounding region of the system, not in the cavities (or inner part
> or core part). Is there any procedure to solvate the cavities as well as
> surrounding region of the system? Please let me know.
>
>
>
> By the way what I do as follows-
>
>
>
> tleap –f leaprc.ff99SB
>
> X=loadpdb nacid.pdb
>
> addions X Na+ 0
>
> solvateoct X TIP3PBOX 8.0
>
> saveamberparm X nacid_solv.prmtop nacid_solv.inpcrd
>
> savepdb X nacid_solv.pdb
>
>
>
> According to many reference core part as well as surrounding part of a
> system can be solvated by immerge the system into a water box followed by
> remove the coordinates of overlaid water molecules. How to do this in AMBER
> 11?
>
>
>
> With the Best Regards,
>
> Sudarshan.
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Dr. Daniel J. Sindhikara
Institute for Molecular Science
E-mail: sindhikara.gmail.com
Website: http://sites.google.com/site/dansindhikara/
--
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Received on Sat Dec 31 2011 - 17:30:03 PST
