AMBER Archive (2009)

Subject: Re: [AMBER] Docking with Amber

• Previous message: Siddharth Rastogi: "[AMBER] ACE and NME patch: VMD ???"
• In reply to: Jordan, Brad: "[AMBER] Docking with Amber"
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On Mon, Aug 31, 2009, Jordan, Brad wrote:

> Group restraints
> 1.0
> RES 10-110

This is the wrong syntax: there should not be a "-" between the 10 and the
110, rather a space.

> GROUP 1 HAS HARMONIC CONSTRAINTS 1.00000
> GROUP 1 CONSISTS OF RESIDUE97110
>
> Number of atoms in this group = 0

This is a signal that your input was not recognized.

> NSTEP ENERGY RMS GMAX NAME NUMBER
> 1 NAN NAN 0.0000E+00 N 1
>
> BOND = 101.3867 ANGLE = 231.9497 DIHED = 1194.9679
> VDWAALS = ************* EEL = -7343.2759 EGB = nan
> 1-4 VDW = 729.7817 1-4 EEL = 5409.3719 RESTRAINT = 0.0000

The stars and "nan" in the vdw and egb results suggest that something is wrong
with the starting structure -- probably two atoms are on top of each other, or
nearly so. Use a visualization program to inspect your starting coordinates,
and look for bad overlaps.

...good luck...dac

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• Previous message: Siddharth Rastogi: "[AMBER] ACE and NME patch: VMD ???"
• In reply to: Jordan, Brad: "[AMBER] Docking with Amber"
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