Hi Naveen,
My answers are below.
On 19/4/2011, at 12:41 p.m., Naveen Samala wrote:
> I am not able to understand the followings things in MTKpp_0.2.0.pdf
> document. Can anyone please help me in this regard?
>
> 1. In section 16.10.6 Side Chain Model the oxygen atoms of AS1(Aspartic),
> AS2 and GL1 (Glutamic) are set to the type O2 of parm94.dat. I would like to
> know why only the oxygen atoms are set to this type, why not the other atoms
> are set to type that exist in parm94.dat.
Perhaps you mean this series of commands here:
# periods are replaced by spaces internally
setAtomType NAME/AS1/.OD1 NAME/OA
setAtomType NAME/AS1/.OD2 NAME/OA
setAtomType NAME/GL1/.OE1 NAME/OB
setAtomType NAME/GL1/.OE2 NAME/OB
setAtomType NAME/AS2/.OD1 NAME/OC
setAtomType NAME/AS2/.OD2 NAME/OC
This means that the oxygen types in AS1, GL1 and AS2, which as you point out are originally O2, are replaced by OA, OB and OC. That's because these oxygen atoms, bonded to the metal ion, need to be given non-standard types. The other atoms in the aspartate and glutamate residues keep their original types, which come from parm94.dat.
> 2. In section 16.10.6 Side Chain Model , what do the terms bd, ag, tr,
> and 87.0 mean in the following line of code?
> addFragment terminal/CH3 bd /NAME/CLR/HD1-1/.CB. ag /NAME/CLR/HD1-1/.CG. tr
> /NAME/CLR/HD1-1/.ND1 87.0
They stand for "bond", "angle" and "torsion" respectively. The bond, angle and torsion are used to position the new fragment (a methyl group, in this case) relative to the three atoms provided (in this case, the beta carbon, gamma carbon and delta nitrogen of the histidine residue).
> 3. In section 16.10.6 Side Chain Model , what does the term "not bb" mean in
> below code? addToResidue /NAME/CLR/HD2 /NAME/1/HID-256 not bb
It means "not backbone", i.e., copy every atom in HID 256 except backbone atoms to the new "HD2" residue in the cluster.
> 4. In section 16.10.6 Side Chain Model , in setting gaussian options how to
> decide the number of processors and size of memory needed to run the
> calculations?
> g03nProc 2
> g03Mem 3000MB
That will depend principally on the hardware of your computer. You'll need to find out what normal practice is for running Gaussian at your facility.
Regards,
Ben
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Received on Tue Apr 19 2011 - 11:00:02 PDT
