Fwd: ramd firstRamdAtom

From: Francesco Pietra (chiendarret_at_gmail.com)
Date: Mon Mar 28 2011 - 03:15:56 CDT

Please forget about this mail. Vlad Cojocaru kindly remainded me to
look at the the topology for the atom id. I was reaaly short of


---------- Forwarded message ----------
From: Francesco Pietra <chiendarret_at_gmail.com>
Date: Mon, Mar 28, 2011 at 9:22 AM
Subject: ramd firstRamdAtom
To: NAMD <namd-l_at_ks.uiuc.edu>


Although I already had experience with the external tcl script  for
RAMD, I forgot the need of

• ramd firstRamdAtom < First index of ligand atom >
Acceptable Values:
positive integer
Specifies the index of the first ligand atom.

It turns out that by vmd-combine of files, now the ligand is at the
bottom of the equilibrated file for the complex protein-ligand. In
between the protein and the ligand lie the membrane, ions, and water,
largely exceeding atom id 99999. Thus, the ligand has "0" for atom id,
such as for its first atom:

219372 ATOM      0  N   AP1 A   1      -2.261  -0.126 -23.292  1.00
0.00      AP   N

where 219372 is the editor line number.

I wonder whether there is a way to recover this long equilibration by
either getting atom id for the ligand or other trick. It is understoon
that I have to restart from ...restert.coor   ..restart.vel.
.restart.xsc...restart.colvars and the starting .psf/.pdb, so that it
would be uneasy for me to modify manually the files.

In detail: .psf/.pdb for the complex come from merging .psf/.pdb for
the aligned protein and aligned ligand, which places the ligand at the
end, after membrane, ions, water.

Thanks for advice.
francesco pietra

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