Dear Pengfei
Thank you so much for the new links.
I will install it tomorrow on my computer and Im eager to check pyMSMT new
results.
Have a nice day!!!
thank you so much,
Vince
2016-04-10 4:42 GMT+02:00 Pengfei Li <ambermailpengfei.gmail.com>:
> Dear Vince,
>
> I checked and found the version 1.0 of pyMSMT released online (
> https://github.com/Amber-MD/pymsmt/releases/tag/v1.0 <
> https://github.com/Amber-MD/pymsmt/releases/tag/v1.0>) could be
> compatible with Amber11, Amber12, and Amber14. It uses a periodic table in
> ParmEd and the path of that periodic table doesn’t change between these
> versions and AmberTools15. So you can try to install this version on your
> computer.
>
> Kind regards,
> Pengfei
>
> > On Apr 9, 2016, at 10:29 AM, Pengfei Li <ambermailpengfei.gmail.com>
> wrote:
> >
> > Dear Vince,
> >
> > MCPB.py is only available in AmberTools15 or higher version. It may not
> be compatible with Amber12 and AmberTools14. Here is a tutorial about
> MCPB.py: http://ambermd.org/tutorials/advanced/tutorial20/mcpbpy.htm <
> http://ambermd.org/tutorials/advanced/tutorial20/mcpbpy.htm>.
> >
> > There is updated version of MCPB.py based on the one in AmberTools15 you
> can download from here: https://github.com/Amber-MD/pymsmt/releases <
> https://github.com/Amber-MD/pymsmt/releases>.
> >
> > If you have any questions, please tell me.
> >
> > Kind regards,
> > Pengfei
> >
> >> On Apr 8, 2016, at 7:42 PM, Vasantha Kumar <vin.vasanth.gmail.com
> <mailto:vin.vasanth.gmail.com>> wrote:
> >>
> >> Dear David
> >>
> >> My peptide is modified, 2HIS (mutated) and 2CYS (regular) coordinated to
> >> zinc (II) ion. As per the ZAFF model to handle zinc works well for 20ps
> rMD
> >> nmr structure calculation and metal geometry is fine. When I change the
> >> total time of rMD to 40ps or higher then metal geometry shows deviation.
> >>
> >> Is this MCPB.py is compatible is compatible with amber 12, amber tool
> 14.?
> >> I would like to give a try with MCPB.py method, therefore I kindly
> request
> >> you to provide me email contact of the author of MCPB.py, so that I can
> >> request related files to handle metal ion. That would be helpful to
> solve
> >> my problem with metal coordination geometry.
> >>
> >> thank you,
> >> Vince
> >>
> >> 2016-04-09 1:29 GMT+02:00 Vasantha Kumar <vin.vasanth.gmail.com
> <mailto:vin.vasanth.gmail.com>>:
> >>
> >>> 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 <mailto:
> 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 <mailto: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 <mailto: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 <mailto:AMBER.ambermd.org>
> >>>>>> http://lists.ambermd.org/mailman/listinfo/amber
> >>>>>>
> >>>>> _______________________________________________
> >>>>> AMBER mailing list
> >>>>> AMBER.ambermd.org <mailto:AMBER.ambermd.org>
> >>>>> http://lists.ambermd.org/mailman/listinfo/amber
> >>>>>
> >>>> _______________________________________________
> >>>> AMBER mailing list
> >>>> AMBER.ambermd.org <mailto:AMBER.ambermd.org>
> >>>> http://lists.ambermd.org/mailman/listinfo/amber
> >>>>
> >>>
> >>>
> >> _______________________________________________
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> >> http://lists.ambermd.org/mailman/listinfo/amber
> >
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Received on Sun Apr 10 2016 - 07:00:03 PDT
