RE: AMBER: restraint value: written but none specified

From: Ross Walker <>
Date: Fri, 20 Apr 2007 15:37:01 -0700

Dear Ben,

> the only difference in setup was the use of solvatecap to
> place 1 water
> molecule
> in 'gap' created by amino acid mutation of M->A and M->G.
> appart from the

And here is your problem - you used the solvatecap command. This will have
added cap information to the prmtop file. This then defines a sphere of
water - in your case a single water. Sander detects the presence of a water
cap and any molecule straying away from the spherical boundary is restrained
back with a harmonic restraint - this is where your restraint is comming
from. It essentially comes from the fact that you used the solvate cap
command for what it was never designed for. I assume you want this water
that you added to be free moving? What other solvent are you using? Are
these GB implicit solvent simulations? If so beware that the GB
implementation may not have been parameterized for simulating "crystal"
waters - just a warning, I digress...

You have two options - 1 is to use your prmtop and inpcrd files to create a
pdb file and then read this back into leap to create a new prmtop and inpcrd
file - thus stripping the label of solvent cap that is attached to the added

Alternatively and the quicker option is just to add IVCAP=2 to the &cntrl
namelist to turn off the cap restraint.

All the best

|\oss Walker

| HPC Consultant and Staff Scientist |
| San Diego Supercomputer Center |
| Tel: +1 858 822 0854 | EMail:- |
| | PGP Key available on request |

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Received on Sun Apr 22 2007 - 06:07:49 PDT
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