RE: AMBER: restraint value: written but none specified

From: Ben Sattelle <>
Date: Sat, 21 Apr 2007 00:05:47 +0100

many thanks for picking up on this,

the solvent is modelled as explicit tip3p. I have just tested IVCAP=2
(and found
it in the manual!), yes, in this case RESTRAINT=0.0. I will also explore
populating the 'gap' by hand (append the water molecule cartesian coordinates
to the pdb and read back into leap).

much appreciated, cheers, Ben.

> 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
> water.
> Alternatively and the quicker option is just to add IVCAP=2 to the &cntrl
> namelist to turn off the cap restraint.
> All the best
> Ross
> /\
> \/
> |\oss Walker
> | HPC Consultant and Staff Scientist |
> | San Diego Supercomputer Center |
> | Tel: +1 858 822 0854 | EMail:- |
> | | PGP Key available on request |
> Note: Electronic Mail is not secure, has no guarantee of delivery, may not
> be read every day, and should not be used for urgent or sensitive issues.
> -----------------------------------------------------------------------
> The AMBER Mail Reflector
> To post, send mail to
> To unsubscribe, send "unsubscribe amber" to

The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" to
Received on Sun Apr 22 2007 - 06:07:50 PDT
Custom Search