Hi Naveen,
On 20 Apr 2011, at 20:55, Naveen Samala wrote:
> Hi,
>
> Please help me in understanding the followings things in
> MTKpp_0.2.0.pdf document.
>
> 1. In Side Chain Model, the oxygen atoms from Aspartic and Glutamic
> Residues bonded to metal ion 'Zn' are given non-standard type. Other atoms
> like oxygen from OH (MOH) and atoms from Histidine residues are also bonded
> to Zn metal ion but not given non-standard type. I would like to know why
> the other atoms are not set to non standard type, if they are also bonded to
> metal ion.
>
> copyAtomType parm94/O2 NAME/OA
> setAtomType NAME/AS1/.OD1 NAME/OA
> setAtomType NAME/AS1/.OD2 NAME/OA
>
Usually it is best to have all bonded atoms set to non standard types and so in theory
you could have a system with multiple metal systems. But it is not compulsory.
These types are used to define bond and angle parameters.
>
> 2. In Side Chain Model, how to know what value to be set for torsion while
> adding Methyl terminating groups?
>
> addFragment terminal/CH3 bd /NAME/CLR/HD1-1/.CB. ag /NAME/CLR/HD1-1/.CG. tr
> /NAME/CLR/HD1-1/.ND1 87.0
>
Unfortunately this part of the approach requires a little user input. You could measure the torsion
between the ND-CG-CB-CA and use that value.
>
> 3. In Large Model, what does the below code mean? (This line is not seen in
> Side Chain Model)
>
> setMaxFileID /NAME/CLR/ /NAME/1
This sets the id of the first atom of /NAME/CLR to the max id of /NAME/1 + 1. This is from the design of
MTK++ where there is only one collection, see docs for more details.
> 4. In Gaussian Options for Large Model, what value should be set for
> Merz-Kollman Radii in case of Iron Metal?
>
> setMKRadii zn 1.1
>
Good question! You might have to search the literature a bit here, sorry I don't have the answer close at hand.
Regards,
Martin.
> Thanks,
> Naveen Samala
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Received on Wed Apr 20 2011 - 15:00:03 PDT
