VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed Jan 14 2015 - 10:44:32 CST

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 

-- 
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