Sinjini,
I see there is already a detailed approach but here is what I was going to
suggest:
(1) Take your system PDB and manually remove the protein chain from it,
save that file;
(2) Run tLEaP as you did before, only use the saved file without the
protein chain in the loadpdb step; and
(3) Make sure you change the names of the prmtop and crd files, you should
now have your system with water (and maybe counterions, too) where the
protein chain was before.
Cheers,
Todd
On Fri, Mar 8, 2024 at 8:10 AM Bhattacharjee, Sinjini via AMBER <
amber.ambermd.org> wrote:
> Dear Amber users,
>
> I want to replace a single protein chain with extra TIP3P waters, in a
> protein-lipid-bilayer box (generated using packmol-memgen).
> Can this be done using tleap without affecting the the original lipids?
>
> Any help or suggestions will be appreciated.
>
>
>
> Best ,
>
> —
> Sinjini Bhattacharjee
>
> PhD Student
> Molecular Theory and Spectroscopy
> Max-Planck-Institut für Kohlenforschung
> 45470 Mülheim an der Ruhr, Germany
>
> email: bhattacharjee.kofo.mpg.de<mailto:bhattacharjee.kofo.mpg.de>
> ---
>
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Received on Fri Mar 08 2024 - 09:00:02 PST
