VMD-L Mailing List

From: JC Gumbart (gumbart_at_ks.uiuc.edu)
Date: Thu Oct 13 2005 - 13:43:01 CDT

Those 5 atoms are your N and C termini, respectively, which Psfgen adds
automatically. However, since it doesn't realize that atoms O1 and O2
can correspond to OT1 and OT2, it ignores them only to regenerate them
anyway (with its best guess for the coordinates of them). The
placement of these atoms is usually not critical anyway, but if you
wish to place the oxygens most accurately, you could change the names
of those two atoms in the pdb.

On Oct 13, 2005, at 1:17 PM, Samuel Flores wrote:

> Hi Guys,
>
> Can anyone tell me why I might be getting 'failed to set coordinate'
> and
> 'poorly guessed coordinates' warnings when reading a pdb? I examined
> the
> structure and found nothing visibly wrong. These were just warnings,
> not
> errors -- still it would be nice to know what's up.
>
> Sam
>
> reading residues from pdb file inputp.pdb extracted 185 residues from
> pdb
> file
> Info: generating structure...
> Info: skipping improper N-C-CA-HN at beginning of segment.
> Info: skipping conformation C-N-CA-C at beginning of segment.
> Info: skipping conformation C-CA-N-HN at beginning of segment.
> Info: skipping bond C-N at end of segment.
> Info: skipping improper C-CA-N-O at end of segment.
> Info: skipping conformation CA-C-N-CA at end of segment.
> Info: skipping conformation N-CA-C-O at end of segment.
> Info: skipping conformation N-CA-C-N at end of segment.
> Info: segment complete.
> reading coordinates from pdb file inputp.pdb for segment U
> Warning: failed to set coordinate for atom O1 PHE:185 U
> Warning: failed to set coordinate for atom O2 PHE:185 U
> Info: guessing coordinates for 1495 atoms (2 non-hydrogen)
> Warning: poorly guessed coordinates for 5 atoms (2 non-hydrogen):
> Warning: poorly guessed coordinate for atom HT1 MET:1 U
> Warning: poorly guessed coordinate for atom HT2 MET:1 U
> Warning: poorly guessed coordinate for atom HT3 MET:1 U
> Warning: poorly guessed coordinate for atom OT1 PHE:185 U
> Warning: poorly guessed coordinate for atom OT2 PHE:185 U
>
> -----Original Message-----
> From: owner-vmd-l_at_ks.uiuc.edu [mailto:owner-vmd-l_at_ks.uiuc.edu] On
> Behalf Of
> Jerry Parks
> Sent: Thursday, October 13, 2005 11:22 AM
> To: vmd-l_at_ks.uiuc.edu
> Subject: vmd-l: Interpolation in internal space
>
> How difficult would it be to generate a linear interpolation from one
> conformation to another in internal coordinates and then write out the
> coordinate snapshots? Such a script would be very useful to me.
> Sometimes
> cartesian interpolations just don't make physical sense.
>
> Thanks,
> Jerry Parks
>
> -----------------------------------------------------------------------
> Hi,
> If I understand correctly, what you're asking for is a script
> that will linearly interpolate the atom coordinates between two
> configurations of the same molecule? If I've misunderstood and
> you actually have more than two sets of coordinates (a trajectory for
> example)
> then you can use the Extensions->Visualization->Movie Maker tool to
> make trajectory animations of your simulation. If you indeed are
> asking for a script that does linear interpolation of atom coordinates,
> I don't have such a script handy but it would be easy to write if
> that's what you're actually after.
>
> John
>
> On Wed, Oct 12, 2005 at 01:58:55PM -0400, Mingliang Tan wrote:
>> Dear all,
>>
>> I would like to know how to show a movie from one static configuration
>> (pdb file available) of a protein to another (pdb file available too),
>> i.e., is there any way to have a movie showing the intermediate
>> structures in VMD?
>>
>> Thank you very much in advance,
>>
>> Mingliang
>
> --
> NIH Resource for Macromolecular Modeling and Bioinformatics
> Beckman Institute for Advanced Science and Technology
> University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> Email: johns_at_ks.uiuc.edu Phone: 217-244-3349
> WWW: http://www.ks.uiuc.edu/~johns/ Fax: 217-244-6078
>