AMBER Archive (2009)

Subject: [AMBER] AMBER: chiral restraint on protein

From: amit jain (amitgood_at_gmail.com)
Date: Tue Feb 10 2009 - 18:48:12 CST

Hello all,I am trying to run some implicit solvent simulation of polyalanine
(with some other AA mutation)
I wish to run replicas in temp range 260-700 K.
After going through tutorial Replica Exchange Simulations with AMBER 10
TUTORIAL A7,
using makeCHIR_RST gives
<http://ambermd.org/tutorials/advanced/tutorial7/files/ala10_chir.dat>
ala10_chir.dat <http://ambermd.org/tutorials/advanced/tutorial7/files/ala10_chir.dat>

#
# chirality for residue 2 atoms: N C HA CB
 &rst iat=7,15,10,11,
   r1=10., r2=60., r3=80., r4=130., rk2 = 10., rk3=10., &end
#
# chirality for residue 3 atoms: N C HA CB
 &rst iat=17,25,20,21, &end
#

Only residue 2 is given r1,r2,r3,r4, rk2, rk3, None of the other residues
were given r values.
Do I have to put in these values by manually going in chir.dat file, Or
there are some default value which it takes for other residues.

Thanks a lot for your reply
Amit
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