Re: seg fault and namdplot problem

From: Cheri M Turman (
Date: Mon Sep 22 2003 - 16:22:46 CDT

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?


   Cheri M. Turman
   Graduate Student
   University of Texas-Houston Medical School
    6431 Fannin
    Houston, TX 77030

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

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