VMD-L Mailing List

From: Francesco Pietra (chiendarret_at_gmail.com)
Date: Sat Jan 10 2015 - 12:12:07 CST

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 [image: $R_1 *
R_2 * 0.6$] of each other, where [image: $R_1$] and [image: $R_2$] 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: 103 (protein) and 499 (none)
Warning) Unusual bond between residues: 133 (protein) and 499 (none)
Warning) Unusual bond between residues: 136 (protein) and 499 (none)
Warning) Unusual bond between residues: 196 (protein) and 499 (none)
Warning) Unusual bond between residues: 230 (protein) and 499 (none)
Warning) Unusual bond between residues: 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