Hello,
ff99SB does not actually have a water residue built into its residue
libraries. The only water residues that are recognized are those from the
water models that are parametrized. If your crystallographic waters did
not cause an error during the save topology file stage, then everything
should be good.
The standard leaprc file for ff99SB (leaprc.ff99SB) makes leap recognize
residue names HOH and WAT as water residues parametrized with whichever
water model you choose (along with TP3), so if this is the case for your
PDB file, there should be no problems.
HTH,
Jason
On Sat, Jan 14, 2012 at 3:44 AM, Sudarshan Debnath <
suarshandebnath.ku.rediffmail.com> wrote:
> Dear all,
>
> I am a user of Amber11. I load a pdb file of nucleic acid including
> the crystal water in
>
> tleap using ff99SB force field. Solvate it with TIP3 water model. Is the
> ff99SB force field
>
> treating the crystal water and TIP3P water as a same way? If not what will
> be done for this?
>
> Please let me know.
>
>
>
> With the best regards,
>
> Sudarshan.
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Sat Jan 14 2012 - 07:00:03 PST
