Hi Abhishek,
The charge and bond information about the standard amino acid residues are stored in the mol2 files under $AMBERHOME/AmberTools/src/pymsmt/lib/ directory, that why you only need to create mol2 files for other residues for MCPB.py processing. Hope it clarifies things.
Kind regards,
Pengfei
> On Nov 12, 2016, at 3:09 AM, Abhi Acharya <abhi117acharya.gmail.com> wrote:
>
> Hi amber users,
>
> I am trying to use the MCPB.py workflow to derive parameters for an active
> site containing Cu2+ and Ca2+ ions. The Cu2+ ion is coordinated by two
> water molecules, and active site residues Asp, His etc.
> My question is that in the input file for MCPB.py do we need to specify
> separate mol2 files for the two water molecules and the coordinating
> residues? In the MCPB.py tutorial at this link:
> http://ambermd.org/tutorials/advanced/tutorial20/mcpbpy.htm the input file
> does not specify any of the coordinating His residues. But still in the 3rd
> step i.e. MCPB.py -i 1OKL.in -s 3, the tutorial says that mol2 files for
> HD1, HD2 and HE1 will be created. I am a bit confused.
>
> I request you to kindly clarify this.
>
> Thanks and Regards,
> Abhishek Acharya
> CFTRI, Mysore.
> _______________________________________________
> 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 Wed Nov 16 2016 - 17:30:02 PST
