Hi,
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.
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
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
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
Thanks,
Naveen Samala
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Received on Tue Apr 19 2011 - 10:00:02 PDT
