Subject: [modeller_usage] Averaged RMSD for 100 models
From: Robert Selwyne <>
Date: Wed, 31 May 2006 11:40:54 +0100 (BST)
Dear Benn
Good Day !!!!!!!!!!!!!
I had run MODELLER to produced model 1-100.pdb (100 models) of same acid sequence but different energy values. Now, i want to calculate the RMSD values for the models. I know that SUPERPOSE will do for me. But i couldnot correlate and implement the results.
Say in VMD 1.8.4 in the RMSD calculator option, if Average is selected, VMD first computes the average x, y, z coordinates of the selected atoms in each molecule, then computes the RMS distance of each molecule from that average structure.
By the same manner, my first model is model1.pdb and now is superpose my model2.pdb and calculate an averaged RMSD. And on the next step i have to superpose my model3.pdb to the averaged structure and calculate new averaged RMSD and so on.
model1.pdb | superposition
| model2.pdb |
now two structures are merged/superposed | calculate the averaged RMSD
for the merged/superposed structure | now superpose model3.pdb to the existing
superposed structure (model1.pdb+model2.pdb) | now totally 3 structures are superposed
| CALCULATE AVERAGED RMSD FOR PRESENT SUPERPOSED STRUCTURE (MODEL1+MODEL2+MODEL3) and so on
Could you please help me in carrying out the problem. can you help me in knowing how the script file looks.
WIth regards robert
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