I think the "bond between ligands were defined" means he is trying to use
harmonic NMR restraints between atoms to mimic the effect of actual
topological harmonic bonds. What
you need, Vince, is Metal Center Parameter Builder (MCPB.py). This
facility is part of the next release of Amber, but you can get it from its
author in my lab. This will automate the quantum calculations to
distribute the charges of the metal center over the atom itself and the
coordinating groups, estimate force constants for bonds that connect the
metal to the rest of the system, and also fill in force constants for the
new angle terms that forming the new bonds implies. MCPB.py will print a
frcmod file and library to feed to tleap so that it knows about your new
"residue" in the metal center. Once Amber knows that these bonds and
angles actually exist, it will count the correct exclusions so that your
simulaion no longer has the metal center crashing into atoms to which it is
bonded. This is what the NMR restraints are not able to do for you.
Dave
On Fri, Apr 8, 2016 at 10:32 AM, Carlos Simmerling <
carlos.simmerling.gmail.com> wrote:
> I don't know which GB model you are using, but I expect that they will not
> work well for many ions, especially ones that are not monovalent. I'm not
> sure I understand the rest of your email about "bond between ligands were
> defined".
>
> On Fri, Apr 8, 2016 at 9:13 AM, Vasantha Kumar <vin.vasanth.gmail.com>
> wrote:
>
> > Dear AMEBR users
> >
> > Is it possible to obtain proper tetrahedral metal geometry for a modified
> > peptide, whose structure was calculated using nmr restraints and using
> > AMBER in restrained MD method.
> > I am currently using non-boded ZAFF model to handle zinc. In my
> calculation
> > of 200ps rMD in GB model metal geometry is deviated from ideal geometry
> > (tetrahedral to trigonal bipyramidal). For the moment I have removed the
> > nmr restraints in the coordination, because on the ligand peaks was not
> > identified due to sever overlap and since bond between ligands were
> > defined. Could any one suggest me in solution NMR structure is it
> possible
> > to maintain geometry in rMD protocol.
> >
> > thanks in advance
> > Vince
> > _______________________________________________
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> > AMBER.ambermd.org
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> >
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Received on Fri Apr 08 2016 - 08:30:03 PDT
