AMBER Archive (2004)

Subject: Re: AMBER: question about the average structure from ptraj

From: Thomas E. Cheatham, III (
Date: Sun Feb 08 2004 - 13:49:23 CST

> I used ptraj to generate average structure for my simulation. I noticed
> the orientation sidechain of one residue was distorted a lot compared with
> initial input structure. However, when I viewed my trajectory file using
> VMD, the sidechain of that residue was in the same orientation as in the
> input file. Anyone has many clues here about what might be the problem?
> ptrajin file is here
> ptraj << EOF
> trajin
> average AR.agonist.average.pdb start 1 stop 200 offset 1 pdb nowrap nobox

The input file above will not best fit the structure hence you may see
smearing of the coordinates due to rotation/translation. It is generally
best to fit the structure (on the region of interest) prior to generating
the average structure.

  rms first mass out ca_rms_to_initial.dat @CA
  average AR.agonist.average.pdb start 1 stop 200 offset 1 pdb nowrap nobox

Good luck,

\ Thomas E. Cheatham, III (Assistant Professor) College of Pharmacy, Depts of
| Medicinal Chemistry and of Pharmaceutics and Pharmaceutical Chemistry
| Adjunct Asst Prof of Bioengineering; Center for High Performance Computing
| University of Utah, 30 South 2000 East, Skaggs 201, Salt Lake City, UT 84112
| (801) 587-9652; FAX: (801) 585-9119
\ BPRP295A / INSCC 418

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