Re: [AMBER] bond distances in amber

From: Mary Varughese <>
Date: Sun, 9 Nov 2014 15:29:20 +0530

thank you sir

On Sun, Nov 9, 2014 at 6:40 AM, David A Case <>

> 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
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Received on Sun Nov 09 2014 - 02:00:02 PST
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