VMD-L Mailing List

From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Tue Jun 22 2010 - 20:16:06 CDT

Hi Emily,
autopsf is not designed to work with coarse grained structures, and
requires some extra care. You cannot tell autopsf to look for protein in
these structures, because CG proteins don't have the usual naming
pattern used to find them. Also, you need to get rid of or change any
terminal patches to match things available in the CG topology file. It
may be easier to manually write a psfgen input for your case, although
if you tell autopsf to work on "everything" and properly modify the
terminal patches things should work ok. Is there anything wrong with the
structure that you get when you check "everything"?

The only unexpected part is vmd crashing occasionally, which definitely
should not happen. Are you able to come up with a sequence of steps that
reproducibly causes the crash?

Best,
Peter

On 06/22/2010 11:32 AM, Emily Chen wrote:
> Hi!
>
> for ikba: (I tried the same thing for ubiquitin)
>
> I started with the file attached: "1IKN.pdb". I used autopsf to create
> a psf file, using the default protein topology (the one that's labeled
> charmm-something). (I checked the protein radio button, and the
> specified the location of my file, if that helps at all.) This worked
> fine. I applied no patches. The end result was "1IKN_autopsf.psf".
>
> I then created a residue based coarse grain model using CG Builder. I
> selected the protein .cgc file but not solvent file. I saved the
> coarse grain coordinates as "Ikbacoarsegrain.pdb", also attached.
> Then, I tried to create a psf file for "Ikbacoarsegrain.pdb" using
> autopsf. I used the "tbcg-2007.top" file as the topology file this
> time, as listed in the documentation link previously. This is when I
> ran into problems:
>
> In the second section, "step 2: selections to include in psf/pdb:"
> if I check "everything", everything works.
> if I check "protein", I get an error:
>
> "Need to have at least one atom in your selection!
> Need to have at least one atom in your selection!
> while executing
> "error "Need to have at least one atom in your selection!" "
> (procedure "write_selection_tempfiles" line 34)
> invoked from within
> "write_selection_tempfiles $currentMol"
> (procedure "::autopsf::aftersels_gui" line 39)
> invoked from within
> "::autopsf::aftersels_gui"
> invoked from within
> ".autopsf.sels.next invoke"
> ("uplevel" body line 1)
> invoked from within
> "uplevel #0 [list $w invoke]"
> (procedure "tk::ButtonUp" line 24)
> invoked from within
> "tk::ButtonUp .autopsf.sels.next"
> (command bound to event)"
>
> If I check everything, and I get to the "create chains" step, I get
> this error:
>
> ERROR: failed on end of segment
> MOLECULE DESTROYED BY FATAL ERROR! Use resetpsf to start over.
> ERROR: failed on end of segment
> MOLECULE DESTROYED BY FATAL ERROR! Use resetpsf to start over.
> while executing
> "segment $segid {
> pdb $segfile
>
> # We alias the C-terminal OXT atoms to OT2 so that psfgen has to
> guess one atom less.
> # Otherwise psf..."
> (procedure "psfsegments" line 37)
> invoked from within
> "psfsegments $logfileout"
> (procedure "::autopsf::afterchains_gui" line 53)
> invoked from within
> "::autopsf::afterchains_gui"
> invoked from within
> ".autopsf.chains.finish invoke"
> ("uplevel" body line 1)
> invoked from within
> "uplevel #0 [list $w invoke]"
> (procedure "tk::ButtonUp" line 24)
> invoked from within
> "tk::ButtonUp .autopsf.chains.finish"
> (command bound to event)
>
> VMD also occasionally crashes when I try to get this to work.
>
> All command line output for the problematic autopsf is attached.
>
> Thank you all for your help!
>
> Emily
>
> On Mon, Jun 21, 2010 at 6:42 PM, Peter Freddolino
> <petefred_at_ks.uiuc.edu <mailto:petefred_at_ks.uiuc.edu>> wrote:
>
> Hi Emily,
> The link that you gave is not to a tutorial, just some
> documentation on the cgtools plugin, so it is not clear exactly
> what you have done. If you can describe step by step what you did
> (starting from what pdb code you're using), we may be able to
> help. Giving a snippet of the pdb file that you're using as input
> to autopsf would also be useful, as would more complete output
> from autopsf.
> Best,
> Peter
>
>
> On 06/21/2010 03:06 PM, Emily Chen wrote:
>> To anyone willing to help,
>>
>> I am learning how to make coarse-grain models.
>> I have generated coarse-grain pdbs using the CG Builder tool. I
>> am trying to create coarse-grain psf files using AutoPSF. I am
>> using the default topology file: "rbcg-2007.top." I am following
>> the directions in this tutorial:
>> http://www.ks.uiuc.edu/Research/vmd/plugins/cgtools/
>>
>> However, the "Create chains" step, I am consistently getting an
>> error:
>>
>> /MOLECULE/ DESTROYED BY FATAL ERROR! /Use resetpsf to start over/.
>>
>> or
>>
>> MOLECULE MISSING! Use resetpsf to start over.
>>
>> MOLECULE MISSING! Use resetpsf to start over.
>> while executing
>> "topology ${basename}-temp.top"
>> (procedure "::autopsf::afterchains_gui" line 22)
>> invoked from within
>> "::autopsf::afterchains_gui"
>> invoked from within
>> ".autopsf.chains.finish invoke"
>> ("uplevel" body line 1)
>> invoked from within
>> "uplevel #0 [list $w invoke]"
>> (procedure "tk::ButtonUp" line 24)
>> invoked from within
>> "tk::ButtonUp .autopsf.chains.finish"
>> (command bound to event)
>>
>> I have tried this for ubiquitin and Ikba, and both of them stop
>> working at that point. Could you give me some direction about
>> what to do, point me to a tutorial, or list some molecules that
>> would work? Thank you so much!
>>
>> Sincerely,
>> Emily Chen
>>
>