Re: [AMBER] bond distances in amber

From: David A Case <>
Date: Sat, 8 Nov 2014 20:10:50 -0500

On Sat, Nov 08, 2014, Mary Varughese wrote:
> I got some valuable information. i am really thankful for the reply.
> sir, if the parm10.dat provides C1'-N9 equillibrium distance as 1.475
> angstrom why 1.52 angstrom in the pdb file i saved from xleap with ff10
> sourced (residue A: RNA Adenine)?

xleap does not change the input coordinates (other than in some cases to
center the molecule in a box). So, the bond length you get when you save
a pdb file in leap will be whatever value that bond length had in the input
PDB file.

If you follow up with a minimization, you should see the C1'-N9 bond length
move closer to the equilibrium distance specified in the parm10.dat file.

If you didn't load a pdb file, but just used the coordinates in the input
library, the same logic holds: all you are seeing is the (somewhat odd)
C1'-N bond length in the standard library. The origin of these coordinates
is lost in the mist of pre-history (generated sometime in the 1980's?).
Again, you should try a minimization and see what happens.

...good luck...dac

AMBER mailing list
Received on Sat Nov 08 2014 - 17:30:02 PST
Custom Search