AMBER Archive (2007)

Subject: AMBER: Fwd: ptraj with protein-ligand

From: Francesco Pietra (chiendarret_at_yahoo.com)
Date: Sun Dec 09 2007 - 04:18:24 CST

Probably a big mistake: the ligand was parameterized with antechamber, while
the atom list was with atoms in uppercase letters only. Should I add the lower
case labels for antechamber?

All that under the prospect that the ligand may adpt to the protein and
possibly also change pocket. As it is, it comes from DOCK6.1.

 Thanks
francesco pietra
--- Francesco Pietra <chiendarret_at_yahoo.com> wrote:

> Date: Sun, 9 Dec 2007 02:11:30 -0800 (PST)
> From: Francesco Pietra <chiendarret_at_yahoo.com>
> Subject: ptraj with protein-ligand
> To: Amber <amber_at_scripps.edu>
>
> I modified the script
>
> measure_equi_rms.ptraj
>
> of tutorial A3 by adding atom O. That in the hope that the
> non-covalently-bound
> non-polymeric large ligand is also taken into account. Is that correct?
>
> Actually, I have so far carried out equilibration (1000 ps in two different
> runs) by restraining protein, its ligand, and also the heads of POPC of the
> membrane. Therefore, that trajin command was just a curiosity. The xmgrace
> plot
> does not show leveling out, which seems to me obvious.
>
> summary for density temp etot were quite OK already after 50-150 ps.
>
> Thanks
>
> francesco pietra
>
>
>
>
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