Difference between revisions of "Hemochromatosis gromacs energy table pictures"

Latest revision as of 17:50, 25 June 2012

Tables

**Table TODO**: TODO
Mutation	Step	Bond	Potential
charmm27foldX_A162S	416.000000	911.913208	-38642.117188
charmm27foldX_A162S_WT	414.000000	912.089478	-38686.621094
charmm27foldX_C282S	434.000000	913.239929	-38589.964844
charmm27foldX_C282S_WT	500.000000	924.356506	-38874.335938
charmm27foldX_E277K	430.000000	911.529053	-38557.769531
charmm27foldX_E277K_WT	459.000000	915.498230	-38748.359375
charmm27foldX_G93R	399.000000	918.111633	-39702.589844
charmm27foldX_G93R_WT	384.000000	909.011108	-38604.292969
charmm27foldX_L183P	414.000000	915.552612	-38457.714844
charmm27foldX_L183P_WT	392.000000	911.028076	-38654.937500
charmm27foldX_M35T	409.000000	914.066162	-38787.164062
charmm27foldX_M35T_WT	483.000000	918.399475	-38843.636719
charmm27foldX_Q127H	500.000000	922.999756	-38733.972656
charmm27foldX_Q127H_WT	498.000000	923.042114	-38891.468750
charmm27foldX_R224W	499.000000	918.184448	-37634.843750
charmm27foldX_R224W_WT	423.000000	912.450745	-38684.457031
charmm27foldX_T217I	500.000000	923.034302	-38771.113281
charmm27foldX_T217I_WT	500.000000	920.963379	-38851.589844
charmm27foldX_V53M	500.000000	919.746765	-38904.714844
charmm27foldX_V53M_WT	427.000000	912.595825	-38751.250000
charmm27scwrl_A162S	493.000000	928.129150	-38806.101562
charmm27scwrl_C282S	500.000000	926.424072	-38715.519531
charmm27scwrl_E277K	500.000000	922.746704	-38652.375000
charmm27scwrl_G93R	500.000000	937.159790	-39957.160156
charmm27scwrl_L183P	500.000000	933.260010	-38573.492188
charmm27scwrl_M35T	432.000000	919.643250	-38756.308594
charmm27scwrl_Q127H	488.000000	926.190369	-38716.339844
charmm27scwrl_R224W	500.000000	924.948364	-37588.648438
charmm27scwrl_T217I	500.000000	929.191162	-38751.257812
charmm27scwrl_V53M	500.000000	925.480591	-38804.257812
charmm27scwrl_WT	500.000000	926.869995	-38812.652344

</figtable>

**Table TODO**:TODO.
Mutation	Step	Bond	Angle	Potential
amber03foldX_A162S	500.000000	491.628113	2726.369141	-35122.839844
amber99sb-ildnfoldX_A162S	411.000000	548.428772	2829.568848	-42459.734375
amber03foldX_A162S_WT	465.000000	488.298706	2727.959473	-35008.968750
amber99sb-ildnfoldX_A162S_WT	411.000000	549.143311	2825.947021	-42442.929688
amber03foldX_C282S	461.000000	487.568878	2732.329102	-34902.957031
amber99sb-ildnfoldX_C282S	411.000000	549.390625	2828.051758	-42387.605469
amber03foldX_C282S_WT	436.000000	485.605164	2733.264404	-34935.320312
amber99sb-ildnfoldX_C282S_WT	430.000000	549.207642	2828.042480	-42433.660156
amber03foldX_E277K	411.000000	483.082153	2733.909424	-34586.335938
amber99sb-ildnfoldX_E277K	450.000000	549.789795	2826.137451	-42290.179688
amber03foldX_E277K_WT	500.000000	491.365387	2725.939453	-35042.156250
amber99sb-ildnfoldX_E277K_WT	410.000000	549.350708	2826.068848	-42442.281250
amber03foldX_G93R	412.000000	488.639648	2738.803955	-35611.089844
amber99sb-ildnfoldX_G93R	403.000000	557.051208	2834.081543	-43169.542969
amber03foldX_G93R_WT	437.000000	485.531738	2731.121826	-35081.218750
amber99sb-ildnfoldX_G93R_WT	408.000000	549.187622	2825.667236	-42462.242188
amber03foldX_L183P	377.000000	483.799500	2766.614014	-34694.523438
amber99sb-ildnfoldX_L183P	431.000000	551.478882	2860.221436	-42201.164062
amber03foldX_L183P_WT	463.000000	488.210205	2726.013428	-35005.070312
amber99sb-ildnfoldX_L183P_WT	405.000000	547.895203	2824.677490	-42419.527344
amber03foldX_M35T	499.000000	490.753815	2731.586182	-35207.015625
amber99sb-ildnfoldX_M35T	398.000000	548.453735	2834.165283	-42549.324219
amber03foldX_M35T_WT	500.000000	490.350128	2731.472900	-35056.296875
amber99sb-ildnfoldX_M35T_WT	431.000000	551.399170	2830.634766	-42482.703125
amber03foldX_Q127H	443.000000	487.118530	2811.132080	-34757.441406
amber99sb-ildnfoldX_Q127H	437.000000	551.995483	2902.304688	-42259.121094
amber03foldX_Q127H_WT	279.000000	468.112152	2735.121094	-34561.304688
amber99sb-ildnfoldX_Q127H_WT	410.000000	548.062073	2830.985596	-42440.109375
amber03foldX_R224W	484.000000	486.756226	2730.202148	-34353.531250
amber99sb-ildnfoldX_R224W	413.000000	539.858215	2828.609131	-41523.914062
amber03foldX_R224W_WT	449.000000	489.200500	2730.227539	-34956.691406
amber99sb-ildnfoldX_R224W_WT	359.000000	544.189209	2828.104736	-42281.617188
amber03foldX_T217I	454.000000	490.702209	2736.986572	-34824.484375
amber99sb-ildnfoldX_T217I	469.000000	554.951294	2827.989258	-42393.929688
amber03foldX_T217I_WT	469.000000	487.084595	2728.806641	-34984.101562
amber99sb-ildnfoldX_T217I_WT	278.000000	535.512634	2823.761475	-42123.968750
amber03foldX_V53M	468.000000	484.353394	2717.921631	-35002.503906
amber99sb-ildnfoldX_V53M	321.000000	537.884521	2815.856934	-42196.277344
amber03foldX_V53M_WT	499.000000	489.776550	2712.700928	-35080.843750
amber99sb-ildnfoldX_V53M_WT	378.000000	544.699585	2814.333008	-42392.343750
amber03scwrl_A162S	446.000000	489.782104	2719.646729	-34788.820312
amber99sb-ildnscwrl_A162S	477.000000	553.757019	2813.325928	-42418.507812
amber03scwrl_C282S	472.000000	488.935638	2708.616699	-34695.152344
amber99sb-ildnscwrl_C282S	407.000000	548.147949	2805.448975	-42232.640625
amber03scwrl_E277K	479.000000	487.748413	2715.674072	-34448.855469
amber99sb-ildnscwrl_E277K	402.000000	544.935852	2814.166016	-42060.632812
amber03scwrl_G93R	453.000000	493.024719	2714.307373	-35355.242188
amber99sb-ildnscwrl_G93R	468.000000	562.177612	2810.380371	-43178.710938
amber03scwrl_L183P	325.000000	480.905640	2740.796875	-34343.757812
amber99sb-ildnscwrl_L183P	344.000000	544.525330	2831.428955	-41881.765625
amber03scwrl_M35T	397.000000	483.174225	2714.149170	-34749.484375
amber99sb-ildnscwrl_M35T	458.000000	551.421387	2804.754639	-42476.714844
amber03scwrl_Q127H	384.000000	483.427490	2787.176758	-34257.574219
amber99sb-ildnscwrl_Q127H	423.000000	550.531982	2878.031738	-42057.433594
amber03scwrl_R224W	500.000000	489.265625	2709.783447	-34167.886719
amber99sb-ildnscwrl_R224W	499.000000	550.281860	2805.838867	-41575.382812
amber03scwrl_T217I	469.000000	493.073303	2714.950439	-34627.269531
amber99sb-ildnscwrl_T217I	444.000000	551.933533	2810.318848	-42198.093750
amber03scwrl_V53M	374.000000	482.391785	2717.136719	-34590.843750
amber99sb-ildnscwrl_V53M	386.000000	548.273010	2810.422363	-42180.039062
amber03scwrl_WT	400.000000	485.167786	2712.698242	-34643.476562
amber99sb-ildnscwrl_WT	424.000000	548.481323	2805.496094	-42275.007812

</figtable>

Pictures

**Table TODO:** Plots of the energy values (bond, angle and potential) of the model .
M35T	Modelenergies based on the foldX M35T mutation.The used forcefield was Amber03.	Modelenergies based on the scwrl M35T mutation.The used forcefield was Amber03.
V53M	Modelenergies based on the foldX V53M mutation.The used forcefield was Amber03.	Modelenergies based on the scwrlV53M mutation.The used forcefield was Amber03.
Q93R	Modelenergies based on the foldX Q93R mutation.The used forcefield was Amber03.	Modelenergies based on the scwrl Q93R mutation.The used forcefield was Amber03.
Q127H	Modelenergies based on the foldX Q127H mutation.The used forcefield was Amber03.	Modelenergies based on the scwrl Q127H mutation.The used forcefield was Amber03.
A162S	Modelenergies based on the foldX A162S mutation.The used forcefield was Amber03.	Modelenergies based on the scwrl A162S mutation.The used forcefield was Amber03.

**Table TODO:** Plots of the energy values (bond, angle and potential) of the model .
L183P	Modelenergies based on the foldX L183P mutation.The used forcefield was Amber03.	Modelenergies based on the scwrl L183P mutation.The used forcefield was Amber03.
T217I	Modelenergies based on the foldX T217I mutation.The used forcefield was Amber03.	Modelenergies based on the scwrl T217I mutation.The used forcefield was Amber03.
R224W	Modelenergies based on the foldX R224W mutation.The used forcefield was Amber03.	Modelenergies based on the scwrl R224W mutation.The used forcefield was Amber03.
E277K	Modelenergies based on the foldX E277K mutation.The used forcefield was Amber03.	Modelenergies based on the scwrl E277K mutation.The used forcefield was Amber03.
C282S	Modelenergies based on the foldX C282S mutation.The used forcefield was Amber03.	Modelenergies based on the scwrl C282S mutation.The used forcefield was Amber03.

**Table TODO:** Plots of the energy values (bond, angle and potential) of the model .
Wildtypes (Amber03)	Wildtype modelenergies based on the foldX M35T mutation.The used forcefield was Amber03.	Wildtype modelenergies based on the foldX V53M mutation.The used forcefield was Amber03.	Wildtype modelenergies based on the foldX G93R mutation.The used forcefield was Amber03.
	Wildtype modelenergies based on the foldX Q127H mutation.The used forcefield was Amber03.	Wildtype modelenergies based on the foldX A162S mutation.The used forcefield was Amber03.	Wildtype modelenergies based on the foldX L183P mutation.The used forcefield was Amber03.
	Wildtype modelenergies based on the foldX T217I mutation.The used forcefield was Amber03.	Wildtype modelenergies based on the foldX R224W mutation.The used forcefield was Amber03.	Wildtype modelenergies based on the foldX E277K mutation.The used forcefield was Amber03.
	Wildtype modelenergies based on the foldX C282S mutation.The used forcefield was Amber03.	Wildtype modelenergies based on the scwrl method. The used forcefield was Amber03.
Wildtypes (Amber99sb-ildn)	Wildtype modelenergies based on the foldX M35T mutation.The used forcefield was Amber99sb-ildn.	Wildtype modelenergies based on the foldX V53M mutation.The used forcefield was Amber99sb-ildn.	Wildtype modelenergies based on the foldX G93R mutation.The used forcefield was Amber99sb-ildn.
	Wildtype modelenergies based on the foldX Q127H mutation.The used forcefield was Amber99sb-ildn.	Wildtype modelenergies based on the foldX A162S mutation.The used forcefield was Amber99sb-ildn.	Wildtype modelenergies based on the foldX L183P mutation.The used forcefield was Amber99sb-ildn.
	Wildtype modelenergies based on the foldX T217I mutation.The used forcefield was Amber99sb-ildn.	Wildtype modelenergies based on the foldX R224W mutation.The used forcefield was Amber99sb-ildn.	Wildtype modelenergies based on the foldX E277K mutation.The used forcefield was Amber99sb-ildn.
	Wildtype modelenergies based on the foldX C282S mutation.The used forcefield was Amber99sb-ildn.	Wildtype modelenergies based on the scwrl method.The used forcefield was Amber99sb-ildn.
Wildtypes (Charmm27)	Wildtype modelenergies based on the foldX M35T mutation.The used forcefield was Charmm27.	Wildtype modelenergies based on the foldX V53M mutation.The used forcefield was Charmm27.	Wildtype modelenergies based on the foldX G93R mutation.The used forcefield was Charmm27.
	Wildtype modelenergies based on the foldX Q127H mutation.The used forcefield was Charmm27.	Wildtype modelenergies based on the foldX A162S mutation.The used forcefield was Charmm27.	Wildtype modelenergies based on the foldX L183P mutation.The used forcefield was Charmm27.
	Wildtype modelenergies based on the foldX T217I mutation.The used forcefield was Charmm27.	Wildtype modelenergies based on the foldX R224W mutation.The used forcefield was Charmm27.	Wildtype modelenergies based on the foldX E277K mutation.The used forcefield was Charmm27.
	Wildtype modelenergies based on the foldX C282S mutation.The used forcefield was Charmm27.	Wildtype modelenergies based on the scwrl method. The used forcefield was Charmm27.

Difference between revisions of "Hemochromatosis gromacs energy table pictures"

Latest revision as of 17:50, 25 June 2012

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@@ Line 9: / Line 9: @@
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 |-
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+| style="border-style: solid; border-width: 1px 1px 1px 1px" |charmm27foldX_A162S
 | style="border-style: solid; border-width: 1px 1px 1px 1px" |416.000000
 | style="border-style: solid; border-width: 1px 1px 1px 1px" |911.913208
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 |-
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+| style="border-style: solid; border-width: 1px 1px 1px 1px" |charmm27foldX_A162S_WT
 | style="border-style: solid; border-width: 1px 1px 1px 1px" |414.000000
 | style="border-style: solid; border-width: 1px 1px 1px 1px" |912.089478
 | style="border-style: solid; border-width: 1px 1px 1px 1px" |-38686.621094
 |-
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+| style="border-style: solid; border-width: 1px 1px 1px 1px" |charmm27foldX_C282S
 | style="border-style: solid; border-width: 1px 1px 1px 1px" |434.000000
 | style="border-style: solid; border-width: 1px 1px 1px 1px" |913.239929
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 |-
-| style="border-style: solid; border-width: 1px 1px 1px 1px" |charmm27foldX_C282S_WT.pdb.tpr.edr.xvg
+| style="border-style: solid; border-width: 1px 1px 1px 1px" |charmm27foldX_C282S_WT
 | style="border-style: solid; border-width: 1px 1px 1px 1px" |500.000000
 | style="border-style: solid; border-width: 1px 1px 1px 1px" |924.356506
 | style="border-style: solid; border-width: 1px 1px 1px 1px" |-38874.335938
 |-
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+| style="border-style: solid; border-width: 1px 1px 1px 1px" |charmm27foldX_E277K
 | style="border-style: solid; border-width: 1px 1px 1px 1px" |430.000000
 | style="border-style: solid; border-width: 1px 1px 1px 1px" |911.529053
 | style="border-style: solid; border-width: 1px 1px 1px 1px" |-38557.769531
 |-
-| style="border-style: solid; border-width: 1px 1px 1px 1px" |charmm27foldX_E277K_WT.pdb.tpr.edr.xvg
+| style="border-style: solid; border-width: 1px 1px 1px 1px" |charmm27foldX_E277K_WT
 | style="border-style: solid; border-width: 1px 1px 1px 1px" |459.000000
 | style="border-style: solid; border-width: 1px 1px 1px 1px" |915.498230
 | style="border-style: solid; border-width: 1px 1px 1px 1px" |-38748.359375
 |-
-| style="border-style: solid; border-width: 1px 1px 1px 1px" |charmm27foldX_G93R.pdb.tpr.edr.xvg
+| style="border-style: solid; border-width: 1px 1px 1px 1px" |charmm27foldX_G93R
 | style="border-style: solid; border-width: 1px 1px 1px 1px" |399.000000
 | style="border-style: solid; border-width: 1px 1px 1px 1px" |918.111633
 | style="border-style: solid; border-width: 1px 1px 1px 1px" |-39702.589844
 |-
-| style="border-style: solid; border-width: 1px 1px 1px 1px" |charmm27foldX_G93R_WT.pdb.tpr.edr.xvg
+| style="border-style: solid; border-width: 1px 1px 1px 1px" |charmm27foldX_G93R_WT
 | style="border-style: solid; border-width: 1px 1px 1px 1px" |384.000000
 | style="border-style: solid; border-width: 1px 1px 1px 1px" |909.011108
 | style="border-style: solid; border-width: 1px 1px 1px 1px" |-38604.292969
 |-
-| style="border-style: solid; border-width: 1px 1px 1px 1px" |charmm27foldX_L183P.pdb.tpr.edr.xvg
+| style="border-style: solid; border-width: 1px 1px 1px 1px" |charmm27foldX_L183P
 | style="border-style: solid; border-width: 1px 1px 1px 1px" |414.000000
 | style="border-style: solid; border-width: 1px 1px 1px 1px" |915.552612
 | style="border-style: solid; border-width: 1px 1px 1px 1px" |-38457.714844
 |-
-| style="border-style: solid; border-width: 1px 1px 1px 1px" |charmm27foldX_L183P_WT.pdb.tpr.edr.xvg
+| style="border-style: solid; border-width: 1px 1px 1px 1px" |charmm27foldX_L183P_WT
 | style="border-style: solid; border-width: 1px 1px 1px 1px" |392.000000
 | style="border-style: solid; border-width: 1px 1px 1px 1px" |911.028076
 | style="border-style: solid; border-width: 1px 1px 1px 1px" |-38654.937500
 |-
-| style="border-style: solid; border-width: 1px 1px 1px 1px" |charmm27foldX_M35T.pdb.tpr.edr.xvg
+| style="border-style: solid; border-width: 1px 1px 1px 1px" |charmm27foldX_M35T
 | style="border-style: solid; border-width: 1px 1px 1px 1px" |409.000000
 | style="border-style: solid; border-width: 1px 1px 1px 1px" |914.066162
 | style="border-style: solid; border-width: 1px 1px 1px 1px" |-38787.164062
 |-
-| style="border-style: solid; border-width: 1px 1px 1px 1px" |charmm27foldX_M35T_WT.pdb.tpr.edr.xvg
+| style="border-style: solid; border-width: 1px 1px 1px 1px" |charmm27foldX_M35T_WT
 | style="border-style: solid; border-width: 1px 1px 1px 1px" |483.000000
 | style="border-style: solid; border-width: 1px 1px 1px 1px" |918.399475
 | style="border-style: solid; border-width: 1px 1px 1px 1px" |-38843.636719
 |-
-| style="border-style: solid; border-width: 1px 1px 1px 1px" |charmm27foldX_Q127H.pdb.tpr.edr.xvg
+| style="border-style: solid; border-width: 1px 1px 1px 1px" |charmm27foldX_Q127H
 | style="border-style: solid; border-width: 1px 1px 1px 1px" |500.000000
 | style="border-style: solid; border-width: 1px 1px 1px 1px" |922.999756
 | style="border-style: solid; border-width: 1px 1px 1px 1px" |-38733.972656
 |-
-| style="border-style: solid; border-width: 1px 1px 1px 1px" |charmm27foldX_Q127H_WT.pdb.tpr.edr.xvg
+| style="border-style: solid; border-width: 1px 1px 1px 1px" |charmm27foldX_Q127H_WT
 | style="border-style: solid; border-width: 1px 1px 1px 1px" |498.000000
 | style="border-style: solid; border-width: 1px 1px 1px 1px" |923.042114
 | style="border-style: solid; border-width: 1px 1px 1px 1px" |-38891.468750
 |-
-| style="border-style: solid; border-width: 1px 1px 1px 1px" |charmm27foldX_R224W.pdb.tpr.edr.xvg
+| style="border-style: solid; border-width: 1px 1px 1px 1px" |charmm27foldX_R224W
 | style="border-style: solid; border-width: 1px 1px 1px 1px" |499.000000
 | style="border-style: solid; border-width: 1px 1px 1px 1px" |918.184448
 | style="border-style: solid; border-width: 1px 1px 1px 1px" |-37634.843750
 |-
-| style="border-style: solid; border-width: 1px 1px 1px 1px" |charmm27foldX_R224W_WT.pdb.tpr.edr.xvg
+| style="border-style: solid; border-width: 1px 1px 1px 1px" |charmm27foldX_R224W_WT
 | style="border-style: solid; border-width: 1px 1px 1px 1px" |423.000000
 | style="border-style: solid; border-width: 1px 1px 1px 1px" |912.450745
 | style="border-style: solid; border-width: 1px 1px 1px 1px" |-38684.457031
 |-
-| style="border-style: solid; border-width: 1px 1px 1px 1px" |charmm27foldX_T217I.pdb.tpr.edr.xvg
+| style="border-style: solid; border-width: 1px 1px 1px 1px" |charmm27foldX_T217I
 | style="border-style: solid; border-width: 1px 1px 1px 1px" |500.000000
 | style="border-style: solid; border-width: 1px 1px 1px 1px" |923.034302
 | style="border-style: solid; border-width: 1px 1px 1px 1px" |-38771.113281
 |-
-| style="border-style: solid; border-width: 1px 1px 1px 1px" |charmm27foldX_T217I_WT.pdb.tpr.edr.xvg
+| style="border-style: solid; border-width: 1px 1px 1px 1px" |charmm27foldX_T217I_WT
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 |}
 </figtable>
 == Pictures ==
 <figtable id="V53M_pymol">