Re: Re: seg fault and namdplot problem

From: Cheri M Turman (
Date: Mon Sep 22 2003 - 18:58:30 CDT

Thanks for the last commments, Jim. I ended up installing csh.
However, new problem...sorry to be such a bother, but I started using
xmgrace which is the new version of xmgr and the plotting would freeze
up not plotting anything/nothing in temp file created. I figured your
namdplot was written for the older version of xmgr so I went and found
4.1.2-10. Now, I get xmgr to open, give the filename as title, put TS
as default on x axis, but nothing on y axis. The terminal gives:
Read ended, non-numeric found on line at or near beginning of file.
Have you used your script with the newer versions of namd? Do you have
quick hint on how to change the namdplot script to account for the
header generated in the namd logfile? I also wonder if xmgr doesn't
like the initial step, gradient tolerance and bracket terms produced
intermittently in the logfile? Thanks for the tips!
   Cheri M. Turman
   Graduate Student
   University of Texas-Houston Medical School
    6431 Fannin
    Houston, TX 77030

    Ph.: 713-500-6126
    Fax: 713-500-0652

----- Original Message -----
From: Jim Phillips <>
Date: Monday, September 22, 2003 6:20 pm
Subject: Re: namd-l: Re: seg fault and namdplot problem

> Hi Cheri,
> First, psfgen guesses H positions based on the IC records in the
> topologyfile or, failing that (since there are no IC records for H
> atoms in the
> top_all22_prot.inp HEME residue), with some very crude rules
> assuming a
> tetrahedral configuration. The goal is to get close enough for the
> minimizer to work. If you use VMD with both the psf and pdb files
> you'llsee the real bonds, but don't make any single-bond
> assumptions based on
> the initial geometry.
> Regarding namdplot, bash has a very different syntax than csh (bash is
> compatible with sh, but only steals features from ksh and csh). If
> youdon't have csh you may have tcsh. If it's not in /bin try
> /usr/bin/ or
> /usr/local/bin (or the unix trick "/bin/env tcsh").
> -Jim
> On Mon, 22 Sep 2003, Cheri M Turman wrote:
> > Hi Jim,
> > You were right about the files I had sent you. I had tried so many
> > things that I couldn't really tell what went with what. However,
> I saw
> > the H coordinates as you said in the pdb file and all were 0. The
> seg> fault was due to these coordinates being 0. I added guesscoor
> after the
> > apoprotein segment and heme segment as you suggested and the H
> then got
> > coordinates assigned. The problem with this is that the heme is
> > distorted as seen in vmd or SPDBViewer. My original psfgen had the
> > guesscoord at this spot which is why they worked before in namd.
> But> when I tried to prevent the heme distortion, I didn't allow
> psfgen to
> > guees coordinates of the heme only the apoprotein. This is when
> the 0.0
> > are generated for the H of the heme. In the distorted heme, it
> appears> as if psfgen is putting hydrogens in a frame where the
> carbons in the
> > heme ring (not part of pyrrole rings, ie. CHC) are sharing the
> hydrogen> with the adjacent carbon in the pyrrole ring (ie. C4B).
> There should be
> > a double bond between these two carbons anyway leaving CHC with
> no room
> > for an H. I cannot figure out why this is occuring. Also, all
> other H
> > (ie. on methyl groups) also form bonds to each other. These are
> both> puzzling me. I have just started to manually modify the H to
> prevent> these bonds in the viewers. Does anyone have comments on
> these problems?
> >
> > Also, Jim, I am trying to run your namdplot script but I keep
> getting> syntax errors. I had to change /bin/csh to /bin/bash so I
> was wondering
> > if my interpreter is not understanding the syntax. I run Debian
> and the
> > bash is suppose to read also csh. The error looked like this:
> >
> > ./namdplot: line 37: syntax error near unexpected token `('
> > ./namdplot: line 37: ` foreach t ( $titles )'
> >
> > Removing the "()" got me further down the program but I had to keep
> > removing these. Finally, at the end it doesn't like how the file
> ends> so I get this error:
> >
> > ./namdplot: line 140: syntax error: unexpected end of file
> >
> > Please let me know your thoughts...should I install an original csh?
> >
> > Thanks,
> > Cheri
> >
> > ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> > Cheri M. Turman
> > Graduate Student
> > University of Texas-Houston Medical School
> > 6431 Fannin
> > Houston, TX 77030
> >
> > e-mail:
> > Ph.: 713-500-6126
> > Fax: 713-500-0652
> >
> >

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