Hi everyone,
Recently I want to simulate Cilengitid, cyclo(R-G-D-f-N[Me]V). I want to
create it in tleap. The only success way I can make the configuration of
amino acids right is using the following commands:
dASP = copy ASP
transform dASP { {1 0 0} {0 1 0} {0 0 -1} }
code = sequence { PHE nmv ARG GLY dASP }
saveamberparm code **.prmtop **.inpcrd
However, after I energy-minimize the structure, the structure seems not
"correct" since the benzene ring of PHE residue locates in the middle of
the cyclic ring (normally it would locates outside the ring as proved by
the crystal structure). I have no idea how I can make this right. Is there
anyone who can fix it? Thx.
P.S. nmv is a residue I created.
Rgds,
C.Q.y
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Received on Wed Apr 24 2013 - 07:30:03 PDT
