VMD-L Mailing List

From: Francesco Pietra (chiendarret_at_gmail.com)
Date: Mon Feb 02 2015 - 14:16:08 CST

John:

Sorry for having missed your mail.

Rather then these two huge systems in periodic TIP3 boxes, I'll try to find
time to build and mail a small system comprising the key issues.

As apparently no one reported failure of VMD on Linux to show bonds listed
in either psf or parm7 files, there must be something wrong with my doing.
However, all other bonds than those alluded to are shown correctly by VMD.
Also, during long MD, the two atoms of such bonds maintain the respective
distances (16 distances in the charmm27 system), while conformational
changes, with changes in other distances occur, as with nearly all MD
simulations.

Thanks
francesco

On Mon, Feb 2, 2015 at 6:30 PM, John Stone <johns_at_ks.uiuc.edu> wrote:

> 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,
> > Ā 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.Ā 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.Ā 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,
> > Ā John Stone
> > Ā [6]vmd_at_ks.uiuc.edu
> >
> > On Sat, Jan 10, 2015 at 07:12:07PM +0100, Francesco Pietra wrote:
> > >Ā Ā Hello:
> > >
> > >Ā Ā From VMD's "What happens when a file is loaded?" one reads "
> If
> > both a PSF
> > >Ā Ā and a PDB file are given, no approximations or guesses are
> made.
> > For those
> > >Ā Ā interested in the details, when VMD is forced to guess the
> > connectivity,
> > >Ā Ā it considers a bond to be formed whenever two atoms are
> within
> > [1]$R_1 *
> > >Ā Ā R_2 * 0.6$ of each other, where [2]$R_1$ and [3]$R_2$ are the
> > respective
> > >Ā Ā radii of candidate atoms."
> > >
> > >Ā Ā As I am forced to use parm7 AMBER files in a new study, is
> any
> > related
> > >Ā Ā info available when laoding .parm7/coordinate files instead
> of
> > .psf/.pdb
> > >Ā Ā files? The very reason for this question, as I am
> experiencing
> > problems
> > >Ā Ā with the minimization: both AMBER Leap (the equivalent of
> psfgen)
> > and
> > >Ā Ā AMBER xparmed.py file analyzer agree that chemical bonds
> that I
> > devised in
> > >Ā Ā Leap between the enzyme backbone and its active center
> > (separately
> > >Ā Ā parameterized) do exist. Nonetheless, such bonds are not
> > displayed by VMD.
> > >Ā Ā Internal bonds within the active center, even involving
> > transition metals,
> > >Ā Ā are correctly displayed by VMD.
> > >
> > >Ā Ā In inserting the active center into the enzyme, the distance
> > between atom
> > >Ā Ā that should result in bonds are
> > >Ā Ā 1.66 2.01 2.56 2.64 3.67 4.09 A
> > >
> > >Ā Ā When loading .parm7/coordinate files, the VM terminal warns
> that
> > >
> > >Ā Ā Warning) Unusual bond between residues:AĀ 103 (protein) and
> 499
> > (none)
> > >Ā Ā Warning) Unusual bond between residues:AĀ 133 (protein) and
> 499
> > (none)
> > >Ā Ā Warning) Unusual bond between residues:AĀ 136 (protein) and
> 499
> > (none)
> > >Ā Ā Warning) Unusual bond between residues:AĀ 196 (protein) and
> 499
> > (none)
> > >Ā Ā Warning) Unusual bond between residues:AĀ 230 (protein) and
> 499
> > (none)
> > >Ā Ā Warning) Unusual bond between residues:AĀ 233 (protein) and
> 499
> > (none)
> > >
> > >Ā Ā where 499 is the active center. I know that "unusual" is
> nothing
> > "unusual"
> > >Ā Ā in this context.
> > >Ā Ā thanks for advice
> > >Ā Ā francesco pietra
> > >
> > > References
> > >
> > >Ā Ā 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/Ā Ā Ā Ā Ā Ā 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/
>