From: Tina Stokelj (tinastokelj_at_gmail.com)
Date: Sat Nov 03 2012 - 09:59:43 CDT
*Hi,*
**
*my name is Tina Štokelj, I am a new NAMD user.*
*I want to investigate the conformational space of dissacharide based on
molecular mechanics simulation. To get an adiabatic conformational map I
need to:*
*1.) restrain two torsion angles psi and phi in the dissacharide molecular
structure, with many combinations (I plan to make a map with grid 19X19)*
*2.) calculate free energy after minimization *
**
*The torsion angles in NAMD may be restrained with Extrabonds file, but I
have to change the values of torsional angles before I run any of the 361
minimizations!*
*It would be nice to cobine torsion restraint with a loop including incr,
such as for example in Tk Console. Keeping one dihedral at the value -180
and increment second dihedral in interval [-180, 180]*
>Main< (cellobiosemin) 71 % set dihed1_atoms {
set one [atomid CARB 1 C4]
set two [atomid CARB 1 O4]
set three [atomid CARB 2 C1]
set four [atomid CARB 2 O5]
}
set one [atomid CARB 1 C4]
set two [atomid CARB 1 O4]
set three [atomid CARB 2 C1]
set four [atomid CARB 2 O5]
>Main< (cellobiosemin) 72 % set init_dihed1 -180
-180
>Main< (cellobiosemin) 73 % set dihed2_atoms {
set one [atomid CARB 1 C5]
set two [atomid CARB 1 C4]
set three [atomid CARB 1 O4]
set four [atomid CARB 2 C1]
}
set one [atomid CARB 1 C5]
set two [atomid CARB 1 C4]
set three [atomid CARB 1 O4]
set four [atomid CARB 2 C1]
>Main< (cellobiosemin) 74 % set init_dihed2 -180
-180
>Main< (cellobiosemin) 75 % for {set init_dihed1 -180; set init_dihed2
-180} {$init_dihed2 < 181} {incr init_dihed1 0; incr init_dihed2 20} {
puts "dihed1: $init_dihed1"
puts "dihed2: $init_dihed2"
}
dihed1: -180
dihed2: -180
dihed1: -180
dihed2: -160
dihed1: -180
dihed2: -140
dihed1: -180
dihed2: -120
dihed1: -180
dihed2: -100
dihed1: -180
dihed2: -80
dihed1: -180
dihed2: -60
dihed1: -180
dihed2: -40
dihed1: -180
dihed2: -20
dihed1: -180
dihed2: 0
dihed1: -180
dihed2: 20
dihed1: -180
dihed2: 40
dihed1: -180
dihed2: 60
dihed1: -180
dihed2: 80
dihed1: -180
dihed2: 100
dihed1: -180
dihed2: 120
dihed1: -180
dihed2: 140
dihed1: -180
dihed2: 160
dihed1: -180
dihed2: 180
>Main< (cellobiosemin) 76 %
Is it possible to increment torsion restrains with loop in Extrabonds or
configuration file before next minimization starts automatically? Is there
any other solution to overcome this problem?
Best regards,
Tina Štokelj
Phd student at University of Trieste
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