AMBER: coordinates ******

From: kepa koldo burusco <>
Date: Tue, 23 Jan 2007 17:19:54 +0100 (CET)


Hi amber users,

I'm running ptraj and carnal calculations over a
trajectory file: RMSD, Radius of Gyration,
Diffusion... using AMBER 7.

The original calculation is a NPT Molecular Dynamics
in CHCL3 solvent and box is a truncated octahedron (by
the way, I am not removing the solvent molecules).

My problem is that restart file (the reference
structure) for RMSD calculations shows a few lines
like the next ones:

 -59.4669830-843.8849945 568.4678259
-61.0471413-843.3087710 567.9562990
 -59.1762415-845.5550610 568.0020731
-59.1694863-843.5231680 570.1622704
  23.1586695************ 614.6020183
22.5738716************ 615.3055373
  21.2429737************ 615.9048135
23.5204386************ 616.6988130
614.2842942-122.6893699-820.1606461 566.1282299
565.7821031-121.8842289-818.0902659 565.2730474
567.2025316-121.1744701-820.7937262 564.4661219

Some of the coordinates are missing and instead a line
of asterisks appears. The problem is that probably the
length of the numerical chain is larger that the
maximum size.

These lines are problematic whenever I try to run
ptraj and carnal. The programs exit when they reach
those lines and print an error message in the logfile.

1) Does anyone know what I can do?
2) Do you think that removing solvent molecules might
3) If I do not center the structures after removing
solvent molecules, do you believe it is still possible
to perform trustworthy diffusion analysis on the bare

Thank you very much in advance!!

Kepa K. Burusco

PhD Student
Universidad Autonoma de Barcelona

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Received on Wed Jan 24 2007 - 06:07:39 PST
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