protein_RNA simulation

From: sripad chandan (sripadchandan_at_gmail.com)
Date: Sat Mar 01 2008 - 08:43:22 CST

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Hii friends,
I want to do simulation of a RNA-peptide complex using NAMD in water
sphere.
Till now I am successful in doing the simulation of both separately in
different files.
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
1.8873
-43609.0745 99999999.9999 31.7079 0.0000
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
VDW energy.

I am attaching .pgn and . conf file.

hope someone can help me.

thanking

chandan

-- 
Sripad Chandan Patnaik
Research Scholar
National Institute of Technology, Rourkela
+91-9861668977

• application/octet-stream attachment: xmin.conf

• text/plain attachment: comp.pgn.txt

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