From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed Jan 21 2015 - 12:28:06 CST

Francesco,

On Wed, Jan 21, 2015 at 06:52:10PM +0100, Francesco Pietra wrote:
> John:
>
> VMD will not guess them, and this would be something that we would
> have to address in the parm7 plugin, as it is the parm7 plugin that
> tells
> VMD what bonds are in the file.
>
> hope you will find time for fixing that.

To be clear, it's not obvious to me if the bonds that you say are missing
are even stored in the parm7 file, in which case this gets to be quite
non-trivial. Can you send us a copy of the parm file(s) that exhibit
the problem you're describing? Without a copy of the actual files, I can't
say whether the AMBER tools are saving this information or just determining
it on-the-fly for themselves.

> The only problem is when
> rendering is needed. The bonds between the protein backbone and the active
> center (carbon-carbon single bonds), commanded on leap, do exist in the
> standar form of tree figures. Still not diplayed on VMD (1.9.1).
> regards
> francesco

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

> On Wed, Jan 14, 2015 at 5:44 PM, John Stone <[1]johns_at_ks.uiuc.edu> wrote:
>
> Francesco,
> A When you load AMBER parm7 files that have bond information, VMD will
> not guess bonds and _only_ the bonds specified in the file will be used.
> If there are bonds implied in the model but not specified in the parm7
> file
> itself, VMD will not guess them, and this would be something that we
> would
> have to address in the parm7 plugin, as it is the parm7 plugin that
> tells
> VMD what bonds are in the file.A The automatic bond determination code
> in
> VMD is deactivated when a plugin like parm7 tells it that it is
> supplying
> all bond info, so any bonds that are missing from your parm7 file are
> something that the parm7 plugin should have found either by reading
> them explicitly, or in the case of some special implied bonds, by doing
> its own internal bond determination logic specific to the parm7 file.
> If you want to have a look at the parm7 plugin, you can see how it gets
> its bond information.A The parm7 file format is largely
> straightforward,
> so it should be easy for you check whether there are extra fields the
> newer versions of AMBER might be saving that the plugin isn't currently
> reading, for example.
>
> Cheers,
> A John Stone
> A [2]vmd_at_ks.uiuc.edu
>
> On Sat, Jan 10, 2015 at 07:12:07PM +0100, Francesco Pietra wrote:
> >A A Hello:
> >
> >A A From VMD's "What happens when a file is loaded?" one reads " If
> both a PSF
> >A A and a PDB file are given, no approximations or guesses are made.
> For those
> >A A interested in the details, when VMD is forced to guess the
> connectivity,
> >A A it considers a bond to be formed whenever two atoms are within
> [1]$R_1 *
> >A A R_2 * 0.6$ of each other, where [2]$R_1$ and [3]$R_2$ are the
> respective
> >A A radii of candidate atoms."
> >
> >A A As I am forced to use parm7 AMBER files in a new study, is any
> related
> >A A info available when laoding .parm7/coordinate files instead of
> .psf/.pdb
> >A A files? The very reason for this question, as I am experiencing
> problems
> >A A with the minimization: both AMBER Leap (the equivalent of psfgen)
> and
> >A A AMBER xparmed.py file analyzer agree that chemical bonds that I
> devised in
> >A A Leap between the enzyme backbone and its active center
> (separately
> >A A parameterized) do exist. Nonetheless, such bonds are not
> displayed by VMD.
> >A A Internal bonds within the active center, even involving
> transition metals,
> >A A are correctly displayed by VMD.
> >
> >A A In inserting the active center into the enzyme, the distance
> between atom
> >A A that should result in bonds are
> >A A 1.66 2.01 2.56 2.64 3.67 4.09 A
> >
> >A A When loading .parm7/coordinate files, the VM terminal warns that
> >
> >A A Warning) Unusual bond between residues:AA 103 (protein) and 499
> (none)
> >A A Warning) Unusual bond between residues:AA 133 (protein) and 499
> (none)
> >A A Warning) Unusual bond between residues:AA 136 (protein) and 499
> (none)
> >A A Warning) Unusual bond between residues:AA 196 (protein) and 499
> (none)
> >A A Warning) Unusual bond between residues:AA 230 (protein) and 499
> (none)
> >A A Warning) Unusual bond between residues:AA 233 (protein) and 499
> (none)
> >
> >A A where 499 is the active center. I know that "unusual" is nothing
> "unusual"
> >A A in this context.
> >A A thanks for advice
> >A A francesco pietra
> >
> > References
> >
> >A A Visible links
> --
> NIH Center for Macromolecular Modeling and Bioinformatics
> Beckman Institute for Advanced Science and Technology
> University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> [3]http://www.ks.uiuc.edu/~johns/A A A A A A Phone: [4]217-244-3349
> [5]http://www.ks.uiuc.edu/Research/vmd/
>
> References
>
> Visible links
> 1. mailto:johns_at_ks.uiuc.edu
> 2. mailto:vmd_at_ks.uiuc.edu
> 3. http://www.ks.uiuc.edu/~johns/
> 4. tel:217-244-3349
> 5. http://www.ks.uiuc.edu/Research/vmd/

-- 
NIH Center for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
http://www.ks.uiuc.edu/~johns/           Phone: 217-244-3349
http://www.ks.uiuc.edu/Research/vmd/