AMBER Archive (2004)

Subject: RE: AMBER: ptraj

From: Ross Walker (
Date: Thu Jul 08 2004 - 12:01:43 CDT

Dear Wen,

> I am trying to do trajectory analysis using ptraj (matrix).
> My trajectory
> file was generated from AMBER7/sander (PME), and it recorded the
> coordinates of one macromolecule and Na+/Cl- ions (not
> recorded that of
> water molecules).

Can I ask how you managed to obtain an mdcrd file from sander without the
water molecules? I may be mistaken but I don't believe there is an option
for doing this. You normally have to post process your mdcrd file through
either ptraj or carnal to strip the water. Are you sure there no water
molecules in the MDCRD file? Try using the original prmtop file (the one you
used for the simulation).

> I wonder if I should use a topology file
> consisting of
> the molecule and the ions or the molecule only - actually resulted in
> the same error message: Segmentation fault (core dumped).

If you are correct that your mdcrd file only has the macromolecule and the
ions then the prmtop you require should also contain just the macromolecule
and ions. Essentially the number of atoms defined in your prmtop MUST match
the number of atoms in your mdcrd file.

Have you also applied any of the bugfixes. I suspect your problem is in a
mismatch between your prmtop and mdcrd files but it can't help to apply the

The specific ones you want are bugfix: 3 & 29

Alternatively you could try downloading the latest version of ptraj from

You should also test if you can successfully read one of your prtmop files
on it's own.


All the best

|\oss Walker

| Department of Molecular Biology TPC15 |
| The Scripps Research Institute |
| Tel:- +1 858 784 8889 | EMail:- |
| | PGP Key available on request |

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