AMBER Archive (2007)

Subject: AMBER: specifying psi and phi for a dipeptide

From: deepti nayar (deepti.icgeb_at_gmail.com)
Date: Wed Mar 28 2007 - 05:50:28 CST

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
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