RE: [AMBER] Is the variation of C-Cl bond length normal?

From: Ross Walker <>
Date: Tue, 13 Apr 2010 12:57:03 -0700

Dear Shulin,

> I used VMD 1.87 to check the ligand and found that before the NPT
> equilibration, the ligand is well, however, during the equilibration,
> the
> bond length of C-CCl varies, sometimes around 1.75 angstrom, sometimes
> above
> 1.8 angstrom. If this bond length above 1.8 angstrom, for example 1.84
> angstrom, the VMD would not treat it as a bond.
> Is the variation of C-Cl bond length normal? Any suggestions would be

This seems reasonable to me. The variation will be very much a function of
what you used for the parameters of the C-Cl bond. You might want to check
the literature to see what others have used for Chloroform solvents for
example and see how this compares to what you are using. As for VMD it
sounds like you just have it being treated as bond by distance. This is what
happens when you just read in a pdb. The current VMD is not smart enough to
base the bond / no bond cut off on the atomic numbers / VDW radii of the
atoms involved in the bond. Hence why for heavier elements it fails to show
the bonds.

You can solve this by loading the prmtop file and then loading the pdb or
trajectory file into the molecule 'created' by loading this prmtop file.
That way VMD will use the bond topology from the prmtop file rather than
trying to calculate it.

All the best

|\oss Walker

| Assistant Research Professor |
| San Diego Supercomputer Center |
| Tel: +1 858 822 0854 | EMail:- |
| | |

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Received on Tue Apr 13 2010 - 13:00:04 PDT
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