See this great tutorial
https://ambermd.org/tutorials/basic/tutorial7/index.php
On Mon, 29 Nov 2021 at 10:39, Carlos Simmerling <carlos.simmerling.gmail.com>
wrote:
> You can retain all of the crystal water if desired.
>
> On Sun, Nov 28, 2021, 9:30 PM Huimin Tian <201921150072.mail.bnu.edu.cn>
> wrote:
>
> > Dear all,
> > I have encountered a problem in the tleap program.
> > I delete the water in pdb first, and then add water with tleap (TIP3P),
> > the water molecules in many positions inside the protein will not be
> > added,
> > which will make certain charged residues closer to the active center
> > overcrowded and deviate from their original positions .
> > After 5ns kinetic simulation, the structure did change.
> > These charged residues deviate from their original positions,
> > which may complicate the study of their chemistry. Is this normal? If it
> > is not normal, what should be done?
> > Should I choose to retain water molecules near charged residues? How to
> > choose which water molecules to retain? Are there general guidelines?
> > Or is there a way to make tleap add water directly to these positions to
> > be consistent with the water in the crystal structure?
> >
> >
> > Thanks and Regards,
> > Tian
> >
> >
> >
> >
> >
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Alan Silva 🚲🏊♂🏃♂🇧🇷🇫🇷🇬🇧
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Nov 30 2021 - 02:00:02 PST
