AMBER Archive (2008)

Subject: AMBER: makeDIST_RST computation of r3 value with IAT < 0

From: Ryan Pavlovicz (pavlovicz.7_at_osu.edu)
Date: Wed Dec 03 2008 - 17:13:32 CST

Hi again,

While preparing an NMR restraint file with an 8 column input file to the
makeDIST_RST program, i notice that the r3 values that i provide are altered
in the cases of IAT(1) < 0 or IAT(2) < 0. I presume this is done to
compensate for the distance averaging done during group assignment, but can
anyone describe how makeDIST_RST determines the r3 output value based on the
input? I cannot find this described in the AMBER User Manual. Thanks a
lot,

ryan

--------------------------------------------------------------

some example inputs / outputs:

input1:
308 ARG O 312 ALA N 2.70 *3.10*
output1:
# 308 ARG O 312 ALA N 2.70 3.10
&rst
ixpk= 0, nxpk= 0, iat=4657,4714, r1= 2.20, r2= 2.70, r3= *3.10*, r4= 3.60,
&end

input2:
62 ASP QB 281 ALA HA 1.80 *3.50*
output2:
# 62 ASP QB 281 ALA HA 1.80 3.50
&rst
ixpk= 0, nxpk= 0, iat= -1,4236, r1= 1.30, r2= 1.80, r3= *3.93*, r4= 4.43,
igr1= 905, 906,
&end

input3:
62 ASP HA 281 ALA QB 1.80 *4.00*
output3:
# 62 ASP HA 281 ALA QB 1.80 4.00
&rst
ixpk= 0, nxpk= 0, iat= 903, -1, r1= 1.30, r2= 1.80, r3= *4.80*, r4= 5.30,
igr2=4238,4239,4240,
&end

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