From: Shirley Hui (shirleyhui_at_alumni.uwaterloo.ca)
Date: Thu Jul 08 2004 - 18:15:29 CDT
Thanks for the insights from everyone.
It was the incorrect settings for the cellBasisVectors that had caused the
warnings I got (i.e. not all atoms have unique coordinates). I set the
vectors x,y,z to be the slightly bigger than the length of the bounding
water box as suggested and the warnings disappear.
Thanks,
shirley
----- Original Message -----
From: "Shirley Hui" <shirleyhui_at_alumni.uwaterloo.ca>
To: <namd-l_at_ks.uiuc.edu>
Sent: Thursday, July 08, 2004 6:45 PM
Subject: Re: namd-l: Warning: Not all atoms have unique coordinates.
> 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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