VMD-L Mailing List

From: Francesco Pietra (chiendarret_at_gmail.com)
Date: Sat Jan 31 2015 - 15:42:05 CST

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 <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 <johns_at_ks.uiuc.edu>, Francesco Pietra <chiendarret_at_gmail.com>,
VMD Mailing List <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 <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
> 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
> http://www.ks.uiuc.edu/~johns/ Phone: 217-244-3349
> http://www.ks.uiuc.edu/Research/vmd/
>