AMBER Archive (2006)

Subject: Re: AMBER: Building polymer with sequence command

From: David A. Case (
Date: Thu Oct 05 2006 - 19:31:36 CDT

On Thu, Oct 05, 2006, wrote:

> I tried to use sequence to build a polymer structure in leap. Here is the
> error message:
> xleap
> -I: Adding /usr/local/amber9/dat/leap/prep to search path.
> -I: Adding /usr/local/amber9/dat/leap/lib to search path.
> -I: Adding /usr/local/amber9/dat/leap/parm to search path.
> -I: Adding /usr/local/amber9/dat/leap/cmd to search path.
> !FATAL ERROR----------------------------------------
> !FATAL: In file [chirality.c], line 142
> !FATAL: Message: Atom named C2 from PAM did not match !
> !

I think we have been through this before(?) I cannot reproduce the problem
here. Try the simplest sequence:

> loadamberprep polyamine.prepin
> x = sequence { PAM PAM PAM }

Do you still get the error?

Also, the error message posted above does not match the error message in
the "leap.log" file that you attached to your e-mail. This is quite
confusing, since you seem to be running two different versions of leap.

If you still get the problem with the above sequence, be sure to provide
information about what version of Amber you are using, which bugfixes have
been applied, and what compiler and OS you are using.

...good luck...dac

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