From: Shirley Hui (shirleyhui_at_alumni.uwaterloo.ca)
Date: Thu Jul 08 2004 - 17:45:47 CDT
Hello,
When I tried to generate the psf for the L chain of CYC, there was a HETATM
segment for a residue called CYC. This residue was not in the topology file
I used top_all22_prot.inp. When I ran psfgen on this yes, there were
errors.
So I removed the HETATM entries from the PDB. When I ran PSF on this pdb
file, there were no errors. I did view the structure in VMD and it looked
fine.
So now I am wondering if the problem has to do with the fact that I removed
these HETATM entries? Can psf handle HETATM?? What should I in this case?
Is it ok to remove the HETATM for CYC residue? Or should the information for
this residue into the topology file? If so, where would I get information
about this residue??
thanks
shirley
----- Original Message -----
From: "Brian Bennion" <brian_at_youkai.llnl.gov>
To: "Shirley Hui" <shirleyhui_at_alumni.uwaterloo.ca>
Cc: <namd-l_at_ks.uiuc.edu>
Sent: Thursday, July 08, 2004 12:06 PM
Subject: Re: namd-l: Warning: Not all atoms have unique coordinates.
> Hi Shirley,
>
> What did the psfgen ouput say when creating the psf and pdb files?
>
> Have you checked them in VMD?
>
> Also in regards to your cellbasis questions, they have to be a bit bigger
> than the vmd minmax values or the periodic images will be so close to
> each other that it may seen to namd that atoms are on top of each
> other....
>
> But the most common cause of this problem is a pdb file generated by
> psfgen that has two atoms at 0.0 0.00 0.00
> because psfgen could not parse the pdb and topology library appropriately.
>
> Regards
>
> Brian
> On Thu, 8 Jul 2004, Shirley Hui wrote:
>
> > I am trying to run a simulation on the L chain of the protein 1CPC (that
is the pdb code). I "think" I have set everything up correctly, however,
when I run the simulation there are some things that I am a bit concerned
about:
> >
> > 1) I get a warning : Warning: Not all atoms have unique coordinates.
(see second line of output below). This warning appears at each step in the
console when the energies are outputted.
> >
> > 2) When I start the minimization process the energies values show up as
99999999.9999 (see output below). I believe this is because of the warning
above.
> >
> > TCL: Minimizing for 500 steps
> > Warning: Not all atoms have unique coordinates.
> > PRESSURE: 0 8.41609e+22 -7.12353e+19 -2.98843e+20 -7.12353e+19
8.37347e+22 1.063
> > 89e+20 -2.98843e+20 1.06389e+20 8.3925e+22
> > GPRESSURE: 0 8.41609e+22 -7.12353e+19 -2.98843e+20 -7.12353e+19
8.37347e+22 1.06
> > 389e+20 -2.98843e+20 1.06389e+20 8.3925e+22
> > ETITLE: TS BOND ANGLE DIHED
IMPRP
> > ELECT VDW BOUNDARY MISC
KINETIC
> > TOTAL TEMP TOTAL2 TOTAL3
TEMPAVG
> > PRESSURE GPRESSURE VOLUME PRESSAVG
GPRESSAVG
> >
> > ENERGY: 0 966810.4900 404837.2614 2875.3521
77388.4504
> > 99999999.9999 99999999.9999 0.0000 0.0000
0.0000
> > 99999999.9999 0.0000 99999999.9999 99999999.9999
0.0000
> > 99999999.9999 99999999.9999 13.1080 99999999.9999
99999999.9999
> >
> > So my question is why I am getting those warnings (that not all the
atoms have unique coordinates?) This is obviously wrong but I wonder where I
went wrong? Would it have been when I generated the PSF structure? Maybe
my config file is wrong? I'm not really sure where to start to figure out
what is wrong...
> >
> > I have attached my config file.
> >
> > thanks for any insight.
> > shirley
>
> *****************************************************************
> **Brian Bennion, Ph.D. **
> **Computational and Systems Biology Division **
> **Biology and Biotechnology Research Program **
> **Lawrence Livermore National Laboratory **
> **P.O. Box 808, L-448 bennion1_at_llnl.gov **
> **7000 East Avenue phone: (925) 422-5722 **
> **Livermore, CA 94550 fax: (925) 424-6605 **
> *****************************************************************
>
>
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