From: Jim Phillips (jim_at_ks.uiuc.edu)
Date: Tue Sep 23 2003 - 21:44:24 CDT
Hi,
I just added a newer Grace-based namdplot as well as namdstats and
namdpstats (which print energy and pressure statistics) to
http://www.ks.uiuc.edu/Research/namd/utilities/
These also add [from <first>] and [to <last>] options so you can plot or
analyze a segment of the file, such as skipping equilibration.
-Jim
On Mon, 22 Sep 2003, Cheri M Turman wrote:
> 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!
> Cheers,
> Cheri
> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> Cheri M. Turman
> Graduate Student
> University of Texas-Houston Medical School
> 6431 Fannin
> Houston, TX 77030
>
> e-mail: cheri.m.turman_at_uth.tmc.edu
> Ph.: 713-500-6126
> Fax: 713-500-0652
>
> ----- Original Message -----
> From: Jim Phillips <jim_at_ks.uiuc.edu>
> 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: cheri.m.turman_at_uth.tmc.edu
> > > Ph.: 713-500-6126
> > > Fax: 713-500-0652
> > >
> > >
> >
> >
>
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