On 5/17/12 2:51 AM, Banafsheh Mehrazma wrote:
Dear all
I 'd like to do NOE distance restraints; according to the chapter 4 of the
manual;
I should specify a section for [ distance_restraints] :
[ distance_restraints ]
; ai aj type index type’ low up1 up2 fac
10 16 1 0 1 0.0 0.3 0.4 1.0
10 28 1 1 1 0.0 0.3 0.4 1.0
10 46 1 1 1 0.0 0.3 0.4 1.0
16 22 1 2 1 0.0 0.3 0.4 2.5
16 34 1 3 1 0.0 0.5 0.6 1.0
.................................................................
althought I've studied the manual, it is still unclear to me, that how is the
index column defined? what are the numbers (0,1,2,3) implying? what about the
low, up1,up2, fac columns?
All of this information is in the manual, section 4.3.4, under the heading
"Using distance restraints."
With respect to indices:
"The type column should always be 1. As explained in sec. 4.3.4, multiple
distances can contribute to a single NOE signal. In the topology this can be set
using the index column. In our example, the restraints 10-28 and 10-46 both have
index 1, therefore they are treated simultaneously."
With respect to low, up1, and up2:
"The columns low, up1, and up2 hold the values of r0, r1, and r2 from eqn.
4.77."
For fac:
"In some cases it can be useful to have different force constants for some
restraints; this is controlled by the column fac. The force constant in the
parameter file is multiplied by the value in the column fac for each restraint."
-Justin
--
========================================
Justin A. Lemkul, Ph.D.
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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