Yes cpptraj can extract the coordinates and water and write a restart
format that you can use as input coordinates. I don't think you need to
rebuild the system.
On Sun, Nov 7, 2021, 10:00 AM Liao <liaojunzhuo.aliyun.com> wrote:
> The coordinates have changed, but also the water is stripped. Essentially
> I have protein+ligand and would like to restart simulation from selected
> frame.
> Looks like the alternative way to do it is take the parameterized mol2
> ligand and somehow write the new coordinates onto it, or take the new
> coordinates and write the partial charges onto it.
> Or maybe just not strip the water, and have cpptraj extract that frame,
> though I’m not sure if that would work
>
>
> > On Nov 7, 2021, at 5:33 AM, Carlos Simmerling <
> carlos.simmerling.gmail.com> wrote:
> >
> > the best way is to take your original leap input and add the solvate
> > command and rerun.
> > or are you saying that you do not have the inputs used to make the
> original
> > gas phase files?
> >
> >> On Sat, Nov 6, 2021 at 4:16 PM Liao <liaojunzhuo.aliyun.com> wrote:
> >>
> >> Dear Amber community,
> >>
> >> As the title is asking, if I had a gas phase parameter and topology file
> >> and want to solvate it for MD, is there anyway to have tleap do that?
> >> What I used to do is I had to reparameterize the ligand from PDB form
> >> extracted from cpptraj and save it as gaff2 mol2, and that’s pretty time
> >> consuming.
> >>
> >> Thanks.
> >>
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Received on Sun Nov 07 2021 - 08:00:02 PST
