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> 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>:
>
>> 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
>>>>>
>>>> _______________________________________________
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>>>>
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>>> AMBER mailing list
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>>>
>>
>>
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Received on Sat Apr 09 2016 - 07:30:03 PDT
