VMD-L Mailing List

From: Per Jr. Greisen (pgreisen_at_gmail.com)
Date: Mon Oct 29 2007 - 01:55:01 CDT

Hi,

Look at the naming between the topology file and your pdb-file - is G
equivalent to the RESI name from the topology ?

On 10/29/07, Samuel Flores <samuel.flores_at_yale.edu> wrote:
>
> 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."
>
>
> 

-- 
Best regards
Per Jr. Greisen
"If you make something idiot-proof, the universe creates a better idiot."