hi
I am working on simulation of dimers.my molecule is
phe-dehydrophenylalanine. sance dehydrophenylalanine is a non standard
residue, I modeled it in x-leap. now i have to set the bond between
alpha carbon and beta-carbon of dehydro-phe at 0 degrees. also I have
to set psi and phi at 180 degrees. I am adding torsional angle
constraints.
1 PHE PSI +180 +180
1 PHE PSI +180 +180
2 PHE CHI1 -1 +1
the first chain of my dimer is phe and 2nd is dehydro-phe
the chi1 is in dehydro-phe so i can write 2 PHE CHI1 -1 +1
here number 2 in front of PHE denotes that it is 2nd chain and so
changes will be made in 2nd chain. but how should I specify psi and
phi since out of the 4 atoms that make psi and phi, they span both the
chains.
I hope i have made myself clear enough to understand. I just want to
know that whatever number is preceeded by pHE, changes will be made in
that chain only. but then how should i specify psi and phi.
please guide me.
thanks
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
Received on Sun Apr 01 2007 - 06:07:07 PDT
