Dear Calos
GB implicit solvent model with IG=5
Bonds between 2HIS and 2CYS to Zinc metal ion (II), as described in ZAFF
model. I also followed same protocol. For shorter rMD (20ps) coordination
geometry wont change much and I gave tetrahedral geometry, but if I change
rMD total time 40 or 100ps then metal geometry changes. However geometry
visually close to tetrahedral geometry, but when I check in chimera, the
pdbs from 40 or 100ps rMD showed deviation (trigonal bi-pyramidal) in the
metal geometry and not tetrahedral geometry in 20ps rMD.
thank you
Vince
2016-04-08 17:01 GMT+02:00 David Cerutti <dscerutti.gmail.com>:
> 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
> > > _______________________________________________
> > > AMBER mailing list
> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> > >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Apr 08 2016 - 16:30:03 PDT
