VMD-L Mailing List

From: Samuel Flores (samuel.flores_at_yale.edu)
Date: Mon Oct 29 2007 - 01:14:01 CDT

Ok, thanks for the files..

I am having an additional problem when I try to generate the psf
file. I follow the tutorial, only substituting a pdb file with a
single G for the ubq.pdb. It looks like:

ATOM 560 P G A2673 27.750 32.191 24.647 0.50
20.52 P
ATOM 561 OP1 G A2673 28.263 33.582 24.710 0.50
20.48 O
ATOM 562 OP2 G A2673 28.704 31.073 24.544 0.50
20.13 O
ATOM 563 O5' G A2673 26.797 31.968 25.922 0.50
20.65 O
ATOM 564 C5' G A2673 25.594 32.771 25.984 0.50
20.91 C
ATOM 565 C4' G A2673 24.887 32.643 27.310 0.50
20.93 C
ATOM 566 O4' G A2673 23.730 31.765 27.155 0.50
20.69 O
ATOM 567 C3' G A2673 25.707 32.006 28.436 0.50
21.02 C
ATOM 568 O3' G A2673 26.449 33.012 29.118 0.50
21.66 O
ATOM 569 C2' G A2673 24.567 31.512 29.340 0.50
20.95 C
ATOM 570 O2' G A2673 23.905 32.629 29.922 0.50
21.18 O
ATOM 571 C1' G A2673 23.669 30.885 28.263 0.50
20.62 C
ATOM 572 N9 G A2673 24.159 29.584 27.812 0.50
20.22 N
ATOM 573 C8 G A2673 25.190 29.319 26.945 0.50
20.10 C
ATOM 574 N7 G A2673 25.382 28.040 26.747 0.50
19.96 N
ATOM 575 C5 G A2673 24.418 27.411 27.532 0.50
19.80 C
ATOM 576 C6 G A2673 24.110 26.051 27.746 0.50
19.58 C
ATOM 577 O6 G A2673 24.629 24.988 27.279 0.50
19.52 O
ATOM 578 N1 G A2673 23.049 25.865 28.623 0.50
19.47 N
ATOM 579 C2 G A2673 22.356 26.880 29.233 0.50
19.48 C
ATOM 580 N2 G A2673 21.369 26.482 30.045 0.50
19.36 N
ATOM 581 N3 G A2673 22.627 28.165 29.051 0.50
19.68 N
ATOM 582 C4 G A2673 23.654 28.361 28.193 0.50
19.89 C

Then I run the ubq.pgn file, changing only the topology file used,
and get the following:

hurakan:~/tbss.work/RNA samuelflores$ /Applications/VMD\ 1.8.5.app/
Contents/MacOS/startup.command -dispdev text -e ubq.pgn
Info) VMD for MACOSXX86, version 1.8.5 (August 25, 2006)
Info) http://www.ks.uiuc.edu/Research/vmd/
Info) Email questions and bug reports to vmd_at_ks.uiuc.edu
Info) Please include this reference in published work using VMD:
Info) Humphrey, W., Dalke, A. and Schulten, K., `VMD - Visual
Info) Molecular Dynamics', J. Molec. Graphics 1996, 14.1, 33-38.
Info) -------------------------------------------------------------
Info) Multithreading available, 2 CPUs detected.
1.4.5
reading topology file /Users/samuelflores/tbss.work/param/toppar/
toppar_history/c26b1_b2_c27a1_a2/top_all22_prot_na.inp

>>>>>> Combined CHARMM22 All-Hydrogen Topology File for <<<<<<<
>>>>>>>>>>>>>>>> Proteins and Nucleic Acids <<<<<<<<<<<<<<<<<<<
>>>>>>>>>>>>>>>>>>>> September 1998 <<<<<<<<<<<<<<<<<<<<<<<<<<<
>>>>>>> Direct comments to Alexander D. MacKerell Jr. <<<<<<<<<
>>>>>> 410-706-7442 or email: alex,mmiris.ab.umd.edu <<<<<<<<<

Created by CHARMM version 22 1
aliasing residue HIS to HSE
aliasing residue ILE atom CD1 to CD
building segment U
reading residues from pdb file ubqp.pdb
unknown residue type G
extracted 1 residues from pdb file
Info: generating structure...
unknown residue type G
ERROR: failed on end of segment
MOLECULE DESTROYED BY FATAL ERROR! Use resetpsf to start over.

MOLECULE MISSING! Use resetpsf to start over.

MOLECULE MISSING! Use resetpsf to start over.

MOLECULE MISSING! Use resetpsf to start over.

MOLECULE MISSING! Use resetpsf to start over.
vmd >

.. so it doesn't recognize the G. The same happens with a different
topology file. Can you help?

Many thanks,

Sam

On Oct 28, 2007, at 2:56 AM, Per Jr. Greisen wrote:

> Hi,
>
> You can download them here:
>
> http://www.pharmacy.umaryland.edu/faculty/amackere/force_fields.htm
>
>
> On 10/28/07, Per Jr. Greisen <pgreisen_at_gmail.com> wrote:
> Hi,
>
> You can download them here:
>
> http://www.pharmacy.umaryland.edu/faculty/amackere/force_fields.htm
>
>
> On 10/28/07, Samuel Flores <samuel.flores_at_yale.edu> wrote:
> Hi Guys,
>
> Thanks again for the last answer.. haven't touched NAMD in the
> longest time. I have an additional question..
>
> I am trying to model RNA. I see in the archives that I need
> par_all22_prot_na.inp and top_all22_prot_na.inp . However I can't
> find these anywhere! Can you tell me where I can get them?
>
> Sam
>
>
> On Oct 26, 2007, at 10:22 AM, Axel Kohlmeyer wrote:
>
> >
> > On Fri, 26 Oct 2007, Samuel Flores wrote:
> >
> > SF> Hi Guys,
> >
> > hi sam,
> >
> >
> > SF> I wonder if someone could remind me how to play back NAMD
> > trajectories in
> >
> > why don't you remind yourself by looking at the stuff at:
> > http://www.ks.uiuc.edu/Research/vmd/current/docs.html#tutorials
> > ?
> >
> > SF> VMD. I thought I would just load the .pdb, .psf, and .dcd
> > files and hit
> > SF> "play." The protein looks fine but when I load the .dcd file
> > and hit play i
> > SF> see a bunch of white dots dancing around a static pdb
> > structure. Can anyone
> > SF> tells me what I'm doing wrong?
> >
> > you load the .psf file first and then the .dcd file "into"
> > this molecule. the .psf file contains the topology information
> > and atom names etc., the .dcd only the coordinates. you need
> > both for a proper display.
> >
> > cheers,
> > axel.
> >
> > SF>
> > SF> Sam
> > SF>
> >
> > --
> >
> ======================================================================
> > =
> > Axel Kohlmeyer akohlmey_at_cmm.chem.upenn.edu http://
> > www.cmm.upenn.edu
> > Center for Molecular Modeling -- University of Pennsylvania
> > Department of Chemistry, 231 S.34th Street, Philadelphia, PA
> > 19104-6323
> > tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel:
> 1-215-898-5425
> >
> ======================================================================
> > =
> > If you make something idiot-proof, the universe creates a better
> > idiot.
>
>
>
>
> --
> Best regards
> Per Jr. Greisen
>
>
> "If you make something idiot-proof, the universe creates a better
> idiot."
>
>
>
> --
> Best regards
> Per Jr. Greisen
>
> "If you make something idiot-proof, the universe creates a better
> idiot."