Dear users,
I am doing umbrella sampling/wham calculation to get a free energy profile
of some nucleophilic substitution reaction between the enzyme and substrate.
I am using bond distance restraints from 3.2 A to 1.0 A. I use the same
run_script provided by Wang here
[1]
http://projects.eml.org/mcm/people/wang/PMF/tutorial.html (below). My
concern is that he uses a fixed starting coordinate file (btn.crd) for all
simulations even at different restraint values. My understanding is,
particularly with my case, if I need to put a distance restraint at value
2.0 A and my starting coordinate (equilibrated starting structure) is about
3.2A, I assume that is a big jump and it will be very hard to get a smooth
SCF convergence. This will not be the case if I start from the previous
window which is say 1.8 A rather than from 3.2 A. Am I right??
The only difference between my case and his case is that he is using a set
of dihedral angle restraints but I think the same concept applies
#!/bin/tcsh
set number=(-180 -160 -140 -120 -100 -80 -60 -40 -20 0 20 40 60 80 100 120
140 160 180)
foreach N ($number)
sed -e 's/minimum/'$N'/g' umbrella.in > input.in
$AMBERHOME/exe/sander -O -i input.in -o btn_$N.out -p btn.top -c btn.crd -r
btn_$N.xyz -x btn_$N.trj
end
My script
#!/bin/bash
Number=(3.2 3.0 2.8 2.6 2.4 2.2 2.0 1.8 1.6 1.4 1.2 1.0)
for i in ${Number}
do
sed -e 's/minimum/'$i'/g' umbrella.in > input.in
/export/home/nmonama/amber/bin/sander -O -i input.in -o dist_$i.out -p
com_solvated.top -c com_solvated_equil.qmmm.rst -r dist_$i.xyz -x
dist_$i.trj
done
Thanks
Best wishes
Mahmoud
--
*************************************************
Mahmoud E. Soliman
Computational Chemistry & Modeling (PhD)
Department of Chemistry
University of Bath
Bath
BA2 7AY
United Kingdom
[2]
http://people.bath.ac.uk/mess20/
[3]
http://www.bath.ac.uk/person/812559
*********************************************
Mahmoud E. Soliman
Lecturer of pharmaceutical organic chemistry
Pharmaceutical Organic Chemistry Dept.
Faculty of pharmacy
Zagazig University
Zagazig
Egypt
**********************************************
Email:
[4]mess20.bath.ac.uk
[5]meelkot.zu.edu.eg
[6]mahmoudelkot.gmail.com
References
1.
http://projects.eml.org/mcm/people/wang/PMF/tutorial.html
2.
http://people.bath.ac.uk/mess20/
3.
http://www.bath.ac.uk/person/812559
4. mailto:mess20.bath.ac.uk
5. mailto:meelkot.zu.edu.eg
6. mailto:mahmoudelkot.gmail.com
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Received on Fri Apr 15 2011 - 11:00:03 PDT
