AMBER Archive (2009)

Subject: [AMBER] ERROR in ptrajInitializeState(): Attempting ....

From: Siavoush Dastmalchi (
Date: Sat May 30 2009 - 11:06:51 CDT

Dear List,
I am trying to use ptraj and my script has the name of mdcrd files and the action command. I am also providing the prmtop file, but I get the following error massages:
Could not open file (egf_egfr_solvated.prmtop) with mode (r)
ERROR in ptrajInitializeState(): Attempting to open parameter/topology file egf_egfr_solvated.prmtop

My prmtop file looks okay to me, however I need to mention that it is a solvated system and the size of the prmtop file is ~14 Mb. Is there any size limitation for ptraj?
Cheers, Siavoush


From: on behalf of Bill Ross
Sent: Thu 2009/05/28 04:22 .
Subject: Re: [AMBER] problem with MM-PBSA

> I visualized the trajectories, I realized that atoms are moving too far
> making bad bond lengths and angles. Gradually, some of the residues
> (atom by atom) move to new locations still keeping their links (very
> long bonds).

This happens when residues cross the edge of the periodic box and
are translated to the other side. If you are running periodic, search
the archive for 'ptraj image'.


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