If you have a crystal structure, why not just use that?
If you are not happy with the default coordinates assigned when you use the
'sequence' command, your only alternative (with tleap) is to supply the
coordinates yourself (or modify them in the xleap GUI editor).
HTH,
Jason
On Wed, Apr 24, 2013 at 10:20 AM, Changqing Yan <ycqchemical.gmail.com>wrote:
> 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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> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Wed Apr 24 2013 - 09:00:02 PDT
