Re: SMD of TFIIB!

From: JC Gumbart (gumbart_at_ks.uiuc.edu)
Date: Fri Aug 25 2006 - 19:43:34 CDT

To use Dyndom, you need two structures, right? There is actually a
new feature in NAMD, Targeted MD, which might be applicable to your
situation.

See TMD here: http://www.ks.uiuc.edu/Research/namd/2.6b2/ug/
node33.html#SECTION000965

On Aug 24, 2006, at 1:57 PM, jonas condes wrote:

>
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> From: jonas condes <jonamdtf_at_yahoo.com.mx>
> Date: August 18, 2006 2:40:46 PM CDT
> To: namd-l_at_ks.uiuc.edu
> Subject: namd-l: SMD of TFIIB
>
>
>
> Hi, all. Well, I`m performing an SMD of the protein TFIIB. What I
> did at first is a search for a hinge region by using the program
> Dyndom. In this case my output are the values of the dihedral
> angles within the hinge region that are necessary in order to pass
> from one conformation to the other (open-closen or reverse). The
> protein consists of two cyclin subdomains and I want to see if I
> can pass from one conformation to the other. The problem now is
> that I don`t know how to input this information in any NAMD conf.
> file given that the only parameters I can state are the constant
> force: k and the constant velocity pulling: v, in order to direct
> my run in the direction of the dihedrals displacements! How can I
> do this?
> Thanks
>
> * the outputs from my dyndom run are also attached in the message
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> From: majordomo_at_ks.uiuc.edu
> Date: August 18, 2006 2:02:48 PM CDT
> To: jonamdtf_at_yahoo.com.mx
> Subject: Welcome to namd-l
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> (All numbering and residues are taken from first PDB file)
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> DynDom run details
>
> Property Value
> Name
> Conformer 1
> (PDB) 1C9.pdb (E)
> Conformer 2
> (PDB) 1TFBmod14_autopsf.pdb (X)
> Window Length 5
> Minimum ratio 1.0
> Minimum domain size 20
> Domains
>
> Domain Size Backbone RMSD
> (A) Residues
> 1 101 3.96 113 - 207 210 - 215
> 2 97 3.24 208 - 209 216 - 310
> Sequence
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> __________________________________________________
> 1C9.pdb(E) :
> DRAMMNAFKEITTMADRINLPRNIVDRTNNLFKQVYEQKSLKGRANDAIA
> :
> 1TFBmod14_autopsf.pdb(X) :
> SRAMMNAFKEITTMADRINLPRNIVDRTNNLFKQVYEQKSLKGRANDAIA
>
> __________________________________________________
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> _________________________________________204______
> 1C9.pdb(E) :
> SACLYIACRQEGVPRTFKEICAVSRISKKEIGRCFKLILKALETSVDLIT
> :
> 1TFBmod14_autopsf.pdb(X) :
> SACLYIACRQEGVPRTFKEICAVSRISKKEIGRCFKLILKALETSVDLIT
>
> _________________________________________204______
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> __________________________________________________
> 1C9.pdb(E) :
> TGDFMSRFCSNLCLPKQVQMAATXiARKAVELDLVPGRSPISVAAAAIYM
> :
> 1TFBmod14_autopsf.pdb(X) :
> TGDFMSRFCSNLCLPKQVQMAATXiARKAVELDLVPGRSPISVAAAAIYM
>
> __________________________________________________
>
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> __________________________________________________
> 1C9.pdb(E) :
> ASQASAEKRTQKEIGDIAGVADVTIRQSYRLIYPRAPDLFPTDFKFDTPV
> :
> 1TFBmod14_autopsf.pdb(X) :
> ASQASAEKRTQKEIGDIAGVADVTIRQSYRLIYPRAPDLFPTDFKFDTPV
>
> __________________________________________________
>
> ______
> 1C9.pdb(E) : DKLPQL
> :
> 1TFBmod14_autopsf.pdb(X) : DKLPQL
> ______
>
> Domain Pairs
>
> Property Value
> Fixed Domain
> ( blue ) 1
> Moving Domain
> ( red ) 2
> Rotation Angle
> (deg) 106.8
> Translation
> (A) 5.0
> Closure
> (%) 97.1
> Bending Residues
> ( green ) 204 - 219
> Bending Region Analysis
>
> lines cross at centre of rotation
> (Move mouse over image to change conformation)
> RASMOL Script
>
> Download RASMOL script file and run with command
> "rasmol -script <script-filename>"
>
> For further details email : sjh_at_cmp.uea.ac.uk
>
> DynDom Copyright © 2003
>
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> (All numbering and residues are taken from first PDB file)
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> Bending Residue Dihedral Analysis
>
> Residue
> i Residue
> i+1 Distance of hinge axis to residue i in conformer 1
> (A) Distance of hinge axis to residue i in conformer 2
> (A) Change in psi (i)
> (deg) Change in phi (i+1)
> (deg) Angle of psi(i) axis to hinge axis conformer 1
> (deg) Angle of psi(i) axis to hinge axis conformer 2
> (deg) Percentage Progress
> (deg)
> GLU-203 THR-204 26.0 20.3 -144.4 -50.8 48.9 47.2 -108.2
> THR-204 SER-205 23.7 19.4 129.0 -142.7 82.9 60.6 1.1
> SER-205 VAL-206 20.0 18.4 -124.4 45.6 22.3 52.4 57.5
> VAL-206 ASP-207 17.6 16.9 -153.4 18.3 100.1 112.4 -36.9
> ASP-207 LEU-208 14.7 14.2 -36.1 -109.6 78.9 97.9 -59.4
> LEU-208 ILE-209 11.5 15.9 -124.1 -76.3 19.4 61.8 139.8
> ILE-209 THR-210 10.0 13.7 131.5 -176.9 89.5 70.5 -10.7
> THR-210 THR-211 7.0 9.9 -147.9 -67.3 36.1 82.3 -87.9
> THR-211 GLY-212 4.1 11.2 11.8 -24.8 146.7 169.0 12.9
> GLY-212 ASP-213 6.4 11.5 70.5 -60.7 112.9 110.7 -10.1
> ASP-213 PHE-214 8.9 7.7 -16.9 61.0 45.4 81.9 -19.0
> PHE-214 MET-215 7.1 8.2 2.7 -26.0 136.0 158.5 16.1
> MET-215 SER-216 4.4 9.6 -2.6 104.2 19.1 53.4 -71.9
> SER-216 ARG-217 6.9 6.2 94.0 -40.8 120.0 159.3 268.2
> ARG-217 PHE-218 8.3 8.3 28.3 -44.7 97.7 125.4 -7.5
> PHE-218 CYS-219 6.1 8.5 46.9 3.8 138.0 87.6 -8.3
> CYS-219 SER-220 3.1 5.4 13.5 -44.8 156.3 155.7 30.8
>
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> Graph shows rotational transition at bending residues and can be
> used to identify hinge bending residues.
> Probably only informative for interdomain rotations greater than 20
> degrees
>
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> For further details email : sjh_at_cmp.uea.ac.uk
>
> DynDom Copyright © 2003
>

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