From: sripad chandan (sripadchandan_at_gmail.com)
Date: Sat Mar 01 2008 - 08:43:22 CST
I want to do simulation of a RNA-peptide complex using NAMD in water
Till now I am successful in doing the simulation of both separately in
I docked them using Autodock and got the pdb file.
I have created the .psf and .pdb file containing both of them using psfgen.
I have wrap it with a water sphere.
Now i tried to do the MD with out PBC.
( conf file given but i am not sure if it is correct.)
The log file is showing this error.
ETITLE: TS BOND ANGLE DIHED
IMPRP ELECT VDW BOUNDARY
MISC KINETIC TOTAL TEMP
TOTAL2 TOTAL3 TEMPAVG
ENERGY: 0 26192.7891 -1.#IND 1142.6129
-43609.0745 99999999.9999 31.7079 0.0000
-1.#IND 0.0000 -1.#IND -1.#IND 0.0000
INITIAL STEP: 1e-006
GRADIENT TOLERANCE: -1.#IND
sure, I am missing some parameter in the .conf file to define the angle and
I am attaching .pgn and . conf file.
hope someone can help me.
-- Sripad Chandan Patnaik Research Scholar National Institute of Technology, Rourkela +91-9861668977
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