From: John Stone (johns_at_ks.uiuc.edu)
Date: Mon Feb 02 2015 - 11:30:53 CST

Francesco,
  Perhaps you didn't see the last emails on this subject, but in order
for us to determine if this is indeed a VMD issue or simply a lack of
information in the input files, or perhaps a limitation of the AMBER parm
reader plugin, I will need a copy of input files and a VMD saved state
that can reproduce what you are seeing. If you could tar/zip up a set
of input files that reproduces the problem and post them on a web page
somewhere, I will have a look.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Sat, Jan 31, 2015 at 10:42:05PM +0100, Francesco Pietra wrote:
> Hi John:
> I am now preparing a system comprising cubane-type [4Fe4S] oxidized
> clusters, charmm27 ff. With each cluster, Fe is also bound to a CYS SG
> sulfur. Each Fe-SG bond is printed in the psf file (following a correct
> topology and correct patching in text-mode dispdev), as a couple of
> indexes corresponding to the outputted pdb (less one, as VMD starts from
> zero). I can also identify the corresponding Fe and SG atoms, highlighting
> them via CPK. In my hands, VMD fails to display the chemical bond between
> Fe and SG. All other bonds are displayed correctly by VMD.
>
> As my previous post regarding similar problems with parm7 files was met by
> surprise, I wonder whether I am using VMD incorrectly to this respect. I
> am still at 1.9.1 but this can not be the problem.
>
> Thanks for advice about using VMD with bonds in this context.
>
> francesco
>
> ---------- Forwarded message ----------
> From: Francesco Pietra <[1]chiendarret_at_gmail.com>
> Date: Wed, Jan 21, 2015 at 6:52 PM
> Subject: Re: vmd-l: Reading chemical bonds by VMD from AMBER parm7 files
> To: John Stone <[2]johns_at_ks.uiuc.edu>, Francesco Pietra
> <[3]chiendarret_at_gmail.com>, VMD Mailing List <[4]vmd-l_at_ks.uiuc.edu>
>
> 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. 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
> On Wed, Jan 14, 2015 at 5:44 PM, John Stone <[5]johns_at_ks.uiuc.edu> wrote:
>
> Francesco,
> 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. 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. 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,
> John Stone
> [6]vmd_at_ks.uiuc.edu
>
> On Sat, Jan 10, 2015 at 07:12:07PM +0100, Francesco Pietra wrote:
> > Hello:
> >
> > From VMD's "What happens when a file is loaded?" one reads " If
> both a PSF
> > and a PDB file are given, no approximations or guesses are made.
> For those
> > interested in the details, when VMD is forced to guess the
> connectivity,
> > it considers a bond to be formed whenever two atoms are within
> [1]$R_1 *
> > R_2 * 0.6$ of each other, where [2]$R_1$ and [3]$R_2$ are the
> respective
> > radii of candidate atoms."
> >
> > As I am forced to use parm7 AMBER files in a new study, is any
> related
> > info available when laoding .parm7/coordinate files instead of
> .psf/.pdb
> > files? The very reason for this question, as I am experiencing
> problems
> > with the minimization: both AMBER Leap (the equivalent of psfgen)
> and
> > AMBER xparmed.py file analyzer agree that chemical bonds that I
> devised in
> > Leap between the enzyme backbone and its active center
> (separately
> > parameterized) do exist. Nonetheless, such bonds are not
> displayed by VMD.
> > Internal bonds within the active center, even involving
> transition metals,
> > are correctly displayed by VMD.
> >
> > In inserting the active center into the enzyme, the distance
> between atom
> > that should result in bonds are
> > 1.66 2.01 2.56 2.64 3.67 4.09 A
> >
> > When loading .parm7/coordinate files, the VM terminal warns that
> >
> > Warning) Unusual bond between residues:A 103 (protein) and 499
> (none)
> > Warning) Unusual bond between residues:A 133 (protein) and 499
> (none)
> > Warning) Unusual bond between residues:A 136 (protein) and 499
> (none)
> > Warning) Unusual bond between residues:A 196 (protein) and 499
> (none)
> > Warning) Unusual bond between residues:A 230 (protein) and 499
> (none)
> > Warning) Unusual bond between residues:A 233 (protein) and 499
> (none)
> >
> > where 499 is the active center. I know that "unusual" is nothing
> "unusual"
> > in this context.
> > thanks for advice
> > francesco pietra
> >
> > References
> >
> > 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
> [7]http://www.ks.uiuc.edu/~johns/ Phone: [8]217-244-3349
> [9]http://www.ks.uiuc.edu/Research/vmd/
>
> References
>
> Visible links
> 1. mailto:chiendarret_at_gmail.com
> 2. mailto:johns_at_ks.uiuc.edu
> 3. mailto:chiendarret_at_gmail.com
> 4. mailto:vmd-l_at_ks.uiuc.edu
> 5. mailto:johns_at_ks.uiuc.edu
> 6. mailto:vmd_at_ks.uiuc.edu
> 7. http://www.ks.uiuc.edu/~johns/
> 8. file:///tmp/tel:217-244-3349
> 9. 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/