On Tue, 2014-02-25 at 19:48 +0700, Setyanto Md wrote:
> Dear AMBER User and Developer.
>
>
> I read in MCPB manual, (MTKpp.pdf) in page 86,
>
> "# Methyl terminating groups (Add these after all other residue have been
> added)
> addFragment terminal/CH3 bd /NAME/CLR/HD1-1/.CB. ag /NAME/CLR/HD1-1/.CG. tr
> /NAME/CLR/HD1-1/.ND1 87.0
> addFragment terminal/CH3 bd /NAME/CLR/AS2-2/.CB. ag /NAME/CLR/AS2-2/.CG. tr
> /NAME/CLR/AS2-2/.OD2 170.0
> addFragment terminal/CH3 bd /NAME/CLR/AS1-3/.CB. ag /NAME/CLR/AS1-3/.CG. tr
> /NAME/CLR/AS1-3/.OD2 200.0
> addFragment terminal/CH3 bd /NAME/CLR/GL1-4/.CB. ag /NAME/CLR/GL1-4/.CG. tr
> /NAME/CLR/GL1-4/.CD. 288.0
> addFragment terminal/CH3 bd /NAME/CLR/HD2-5/.CB. ag /NAME/CLR/HD2-5/.CG. tr
> /NAME/CLR/HD2-5/.ND1 185.0"
>
> I'd like to know where th number 87.0, 170.0, 200.0, 288.0, 185.0 come from
> ?
I could be mistaken here since, as you've noticed, the documentation is
not at all clear with respect to the addFragment command and I did not
write this code. However, here is my best guess (note that the last
argument 'angle' is missing from the usage statement on page 93 of the
MTK++ manual):
addFragment <fragment> bd <atom1> ag <atom2> tr <atom3> <angle>
<fragment> is the name of the molecule fragment you wish to add
bd is a keyword that indicates the next atom is BonDed to the fragment
<atom1> is the atom that the <fragment> is connected to
ag is another keyword that indicates the next atom forms an AnGle with
the fragment and <atom1>
<atom2> is the atom that the <fragment> forms an angle with <atom1>
tr is another keyword that indicates the next atom forms a ToRsion with
the fragment and <atom1> and <atom2>
<atom3> is the atom that the <fragment> forms a torsional angle with
<atom1> and <atom2>
<angle> is the torsional angle, in degrees, that defines the relative
orientation of the new fragment w.r.t. the atoms 1, 2, 3 and the
fragment.
While I think this is the correct explanation I'm not certain. You'll
have to experiment with different options to determine the accuracy of
my assessment for yourself.
Good luck,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Tue Feb 25 2014 - 05:30:02 PST
