Re: [AMBER] Could tleap read in parameter and restart file instead of PDB or mol2?

From: Liao <>
Date: Sun, 7 Nov 2021 08:59:41 -0600

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 <> 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 <> 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 - 07:30:02 PST
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