From: Tina Stokelj (tinastokelj_at_gmail.com)
Date: Mon Nov 05 2012 - 06:38:32 CST
*Thank you Norman, *
**
*it was a godd idea, I didn't thought about it. I included suggested in
.cfg file, but NAMD only ran the first simulation, with extrabonds file1.
Then an eroor occurs:*
**
*TCL: Setting parameter extrabondsFile to extrabonds2.txt*
*FATAL ERROR: Setting parameter extrabondsFile from script failed!*
**
*I also tried to copy entire script in the .cfg. file twice. As before the
first minimization runs normally, but for the second script the error
occurs:*
**
*FATAL ERROR: setting parameter coordinates from script failed
(Reading coordinates from .pdb file is the first action called in script.) *
**
*I append the content of my extrabonds.txt file:*
**
#Add torsional angle restrain
# dihedral a1 a2 a3 a4 kref
dihedral 1 2 24 28 1. 20.
dihedral 7 1 2 24 1. 180.
*And the content of my configuration file:*
# NAMD Config file - autogenerated by NAMDgui plugin
# Author: Jan Saam, saam_at_charite.de
# input
coordinates tina_solvated.pdb
structure tina_solvated.psf
parameters par_all36_sugar_tip3.inp
paratypecharmm on
# output
set output minimization
outputname $output
dcdfile ${output}.dcd
xstFile ${output}.xst
dcdfreq 50
xstFreq 50
binaryoutput no
binaryrestart no
outputEnergies 100
restartfreq 1000
fixedAtoms off
# Basic dynamics
exclude scaled1-4
1-4scaling 1
COMmotion no
dielectric 1.0
# Simulation space partitioning
switching on
switchdist 10
cutoff 12
pairlistdist 14
# Multiple timestepping
firsttimestep 0
timestep 1
stepspercycle 10
nonbondedFreq 1
fullElectFrequency 2
# Temperature control
set temperature 298
temperature $temperature; # initial temperature
#############################################################
## EXTRA PARAMETERS ##
#############################################################
extraBonds yes
extraBondsFile extrabonds.txt
# Scripting
minimize 3000
*Maybe there is still some other way to do it? *
**
*Best regards, *
*Tina Stokelj*
*PhD at University of Trieste*
On Mon, Nov 5, 2012 at 8:32 AM, Norman Geist <norman.geist_at_uni-greifswald.de
> wrote:
> Hi Tina,****
>
> ** **
>
> first of all you should try some seperate extrabonds files, and a script
> like****
>
> ** **
>
> extrabonds on****
>
> extrabondsfile file1****
>
> minimize 10****
>
> extrabondsfile file2****
>
> minimize 10****
>
> ** **
>
> Of course the files should affect the same atoms. If you see this works
> like expected, you could simply create this extrabondsfiles with the tcl
> interface between the minimize runs.****
>
> ** **
>
> Norman Geist.****
>
> ** **
>
> *Von:* owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] *Im
> Auftrag von *Tina Stokelj
> *Gesendet:* Samstag, 3. November 2012 16:00
> *An:* namd-l_at_ks.uiuc.edu
> *Betreff:* namd-l: increment torsion restrain before minimization****
>
> ** **
>
> *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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