AMBER Archive (2004)

Subject: Re: AMBER: ANAL problem.

From: David A. Case (
Date: Mon Feb 02 2004 - 12:51:02 CST

On Thu, Jan 29, 2004, A.B.S.M Osman gani wrote:
> I have been using AMBER 7 on Red Hat Linux. I have done long dynamic
> simulations in SANDER for a ligand +Protein complex. Then trajectories were
> extracted with ?ptraj?. For energy analysis, ANAL command was performed.
> But the anal output file shows ?DIHEDRAL ANGLE ERROR: 1 12153
> 12138 12141 12147 5 0 0.0000 0.0000?

You have a bad dihedral, but it is not clear whether this is really in the
prmtop file, or whether the anal program is overflowing some array.

The program thinks that the first dihedral, which involves atoms
4052, 4047, 4048, and 4050, (dihedral code "5") has a periodicity of 0;
this is illegal.

Are you using the exact same prmtop file that you used for the dynamics run?
Is there anything special about the above atoms? You say that the
"trajectories were extracted with ptraj", but it is not clear what exactly
you did with ptraj.

You might examine your prmtop file (either by hand, or with rdparm) to look
at the dihedral angles. Also, please post the first ten lines or so of
your prmtop file: it is certainly possible that you are exceeding some
maximum value in anal (you have a very big system) that is not being trapped.



================================================================== David A. Case | e-mail: Dept. of Molecular Biology, TPC15 | fax: +1-858-784-8896 The Scripps Research Institute | phone: +1-858-784-9768 10550 N. Torrey Pines Rd. | home page: La Jolla CA 92037 USA | ================================================================== ----------------------------------------------------------------------- The AMBER Mail Reflector To post, send mail to To unsubscribe, send "unsubscribe amber" to