AMBER Archive (2007)

Subject: AMBER: ptraj with protein-ligand

From: Francesco Pietra (chiendarret_at_yahoo.com)
Date: Sun Dec 09 2007 - 04:11:30 CST

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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