deeing.blogspot.com

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2007년 7월 29일 일요일. Parameterizing a novel residue (NAMD). This is a summary of NAMD turorial, parameterizing a novel residue. Http:/ www.ks.uiuc.edu/Training/Tutorials/science/forcefield-tutorial/linux/forcefield-html-linux/newforcefield.html. Vmd HisH glutamine.pdb. VMD - Graphics: Representations - Selected Atoms. Drawing method - CPK. Segname HISH and resid 84 178 180. Drawing method - licorice. Set sel [atomselect top "resid 84"]. Sel set resname CYG. Set sel2 [atomselect top "segname LIG"]. Set fixed...

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2007년 7월 29일 일요일. Parameterizing a novel residue (NAMD). This is a summary of NAMD turorial, parameterizing a novel residue. Http:/ www.ks.uiuc.edu/Training/Tutorials/science/forcefield-tutorial/linux/forcefield-html-linux/newforcefield.html. Vmd HisH glutamine.pdb. VMD - Graphics: Representations - Selected Atoms. Drawing method - CPK. Segname HISH and resid 84 178 180. Drawing method - licorice. Set sel [atomselect top resid 84]. Sel set resname CYG. Set sel2 [atomselect top segname LIG]. Set fixed...

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1 deeing

2 1 system setup

3 segname lig

4 create rep

5 in vmd tk

6 psfgen

7 myoutput2

8 solvate

9 package require solvate

10 cd long min

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deeing | deeing.blogspot.com Reviews

https://deeing.blogspot.com

2007년 7월 29일 일요일. Parameterizing a novel residue (NAMD). This is a summary of NAMD turorial, parameterizing a novel residue. Http:/ www.ks.uiuc.edu/Training/Tutorials/science/forcefield-tutorial/linux/forcefield-html-linux/newforcefield.html. Vmd HisH glutamine.pdb. VMD - Graphics: Representations - Selected Atoms. Drawing method - CPK. Segname HISH and resid 84 178 180. Drawing method - licorice. Set sel [atomselect top "resid 84"]. Sel set resname CYG. Set sel2 [atomselect top "segname LIG"]. Set fixed...

INTERNAL PAGES

deeing.blogspot.com

1

deeing: NAMD Tutorial 3 (Steered MD)

http://deeing.blogspot.com/2007/07/namd-tutorial-3-steered-md.html

2007년 7월 29일 일요일. NAMD Tutorial 3 (Steered MD). I Removing water Molecules. Load ubq ws.psf and ubq ws eq.restart.coor. Set selprotein [atomselect top proein]. Selprotein writepdb common/ubq ww eq.pdb. II Constant Velocity Pulling. Load common/ubq.psf and common/ubq ww eq.pdb. Set allatoms [atomselect top all]. Allatoms set beta 0. Set fixedatom [atomselect top "resid 1 and name CA"]. Fixedatom set beta 1. Allatoms set occupancy 0. Set smdatom [atomselect top "resid 76 and name CA"]. Save nx, ny, and nz.

2

deeing: NAMD Turtorial 2 (Analysis)

http://deeing.blogspot.com/2007/07/namd-turtorial-2.html

2007년 7월 28일 토요일. NAMD Turtorial 2 (Analysis). 1 Calculating RMSD of indivisual residus and coloring residus by property. Source residu rmsd.tcl. Set sel resid [ atomselect top "protein and alpha"] get resid]. Rmsd residue over time top $sel resid. VMD - Colors - Color Scale - Method - BGR. 2 Maxwell-Boltzmann Energy Distribution. Load ubq ws.psf and ubq ws eq 1fs.restart. Set all [atomselect top all]. Set fil [open energy.dat w]. Foreach m [$all get mass] v [$all get {x y z}] {. 피드 구독하기: 댓글 (Atom).

3

deeing: Parameterizing a novel residue (NAMD)

http://deeing.blogspot.com/2007/07/parameterizing-novel-residue-namd.html

2007년 7월 29일 일요일. Parameterizing a novel residue (NAMD). This is a summary of NAMD turorial, parameterizing a novel residue. Http:/ www.ks.uiuc.edu/Training/Tutorials/science/forcefield-tutorial/linux/forcefield-html-linux/newforcefield.html. Vmd HisH glutamine.pdb. VMD - Graphics: Representations - Selected Atoms. Drawing method - CPK. Segname HISH and resid 84 178 180. Drawing method - licorice. Set sel [atomselect top "resid 84"]. Sel set resname CYG. Set sel2 [atomselect top "segname LIG"].

4

deeing: NAMD tutorial 1 (Basic)

http://deeing.blogspot.com/2007/07/namd-tutorial-1.html

2007년 7월 28일 토요일. NAMD tutorial 1 (Basic). This example is a summary of namd tutorial. Http:/ www.ks.uiuc.edu/Training/Tutorials/]. I Generate PSF from PDB. 1 extract PROTEIN from PDB. Set ubq [atomselect top protein]. Ubq writepdb ubqp.pdb. Vmd -dispdev text -e ubq.pgn. Topology top all27 prot lipid.inp. Pdbalias residue HIS HSE. Pdbalias atom ILE CD1 CD. Segment U {pdb ubqp.pdb}. Coordpdb ubqp.pdb U. II Solvate protein in a sphere or periodic box. Vmd -dispdev text -e wat sphere.tcl. In a VMD Tk).

5

deeing: 7월 2007

http://deeing.blogspot.com/2007_07_01_archive.html

2007년 7월 29일 일요일. Parameterizing a novel residue (NAMD). This is a summary of NAMD turorial, parameterizing a novel residue. Http:/ www.ks.uiuc.edu/Training/Tutorials/science/forcefield-tutorial/linux/forcefield-html-linux/newforcefield.html. Vmd HisH glutamine.pdb. VMD - Graphics: Representations - Selected Atoms. Drawing method - CPK. Segname HISH and resid 84 178 180. Drawing method - licorice. Set sel [atomselect top "resid 84"]. Sel set resname CYG. Set sel2 [atomselect top "segname LIG"]. Set fixed...

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2007년 7월 29일 일요일. Parameterizing a novel residue (NAMD). This is a summary of NAMD turorial, parameterizing a novel residue. Http:/ www.ks.uiuc.edu/Training/Tutorials/science/forcefield-tutorial/linux/forcefield-html-linux/newforcefield.html. Vmd HisH glutamine.pdb. VMD - Graphics: Representations - Selected Atoms. Drawing method - CPK. Segname HISH and resid 84 178 180. Drawing method - licorice. Set sel [atomselect top "resid 84"]. Sel set resname CYG. Set sel2 [atomselect top "segname LIG"]. Set fixed...

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