Re: [AMBER] deletedihedral

From: Jason Swails <>
Date: Tue, 23 Jul 2013 13:03:44 -0400

On Tue, Jul 23, 2013 at 10:52 AM, Aronica, Pietro <> wrote:

> Thank you for your reply.
> Yes, I am aware of the fact that VdW parameters are 0. I guess you could
> call it a prmtop-based FEP scheme, that's not a bad approximation.
> As for the hydrogens being in the "wrong" list, this is deliberate. We
> were having problems with SHAKE interfering with our custom atoms, so we
> needed those bonds to not be considered as including hydrogens. This was
> accomplished by setting the element of the custom hydrogens to gadolinium
> (hence the atomic number of 64), though their mass and other parameters are
> then set to those of a normal hydrogen. The result is that the atoms are
> effectively hydrogens but are not thought of as such when writing the
> prmtop. Perhaps bad practice, but as a workaround it works well enough for
> the moment.
> Is putting them in the "DIHEDRALS INCLUDING HYDROGEN" list the only
> solution?

Ah, I see. I guess ParmEd should be a bit more permissive here. This code
was actually written before the ATOMIC_NUMBER section was added to the
topology file -- as a result the 'element' is always assigned based on the
atomic mass in this particular action. A more flexible approach would be
to look at the mass only if an ATOMIC_NUMBER section does not exist...
 This is easy enough to accomplish.

As an aside, did the "noshakemask" variable not work? In any case, this is
an improvement worth making.

All the best,

Jason M. Swails
Rutgers University
Postdoctoral Researcher
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Received on Tue Jul 23 2013 - 10:30:02 PDT
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