AMBER Archive (2006)

Subject: Re: AMBER: ptraj help - ERROR in readParm: ... failed to find CHARGE

From: Thomas E. Cheatham, III (cheatham_at_chpc.utah.edu)
Date: Fri Mar 31 2006 - 16:18:57 CST

> I am a novice of Amber and wondering if anyone can help me with this
> problem. It is a simple task to try to convert a list of Amber restart
> files to PDB format files using ptraj command. The OS is Linux (cluster)
> and it is Amber version 7. According to the manual the second argument
...
> ERROR in readParm: ...failed to find CHARGE
>
> But when I opened the topology file, apparently there are charges section in
> that file:
>
> %FLAG
> CHARGE
> %FORMAT(5E16.8)

This should work, but obviously is hiccuping if you are seeing this
problem. You could try getting the ptraj version of the WWW site (which
is out of date, but more bug fixed than AMBER7):

        http://www.chpc.utah.edu/~cheatham/software.html

Two issues come to mind:

(1) ptraj is not properly handling the non-determinant order of the
parameters (a bug in the older versions) or

(2) the file was moved from a windows box or to a windows box? If you
did this, there can be extra carriage returns in addition to newline
characters at the ends of lines which confuses earlier versions of ptraj.
You could detect this by doing (on Unix/Linux) od -c prmtop and looking
for \r\n at the end of the lines. The \r can be removed by an editor or a
newer version of ptraj can be used.

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