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
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
3. In Large Model, what does the below code mean? (This line is not seen in
Side Chain Model)
setMaxFileID /NAME/CLR/ /NAME/1
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
Thanks,
Naveen Samala
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Received on Wed Apr 20 2011 - 13:00:03 PDT
