AMBER Archive (2009)

Subject: [AMBER] Restrained backbone conformation MD simulation"

From: Prem Prakash Pathak (prempolymer_at_gmail.com)
Date: Fri Jul 10 2009 - 06:27:38 CDT

Dear Amber users,

what do i understand from the word "Restrained backbone conformation MD
simulation"

i wanted to do salt bridge analysis of protein solved by NMR.

Some have mentioned that they have done 5ps Restrained backbone conformation
MD simulation to analyse the rotamers.

what does this mean.

1. is it that one has to use NMR restrains.

2. is it that we have to use simple wt function
like
Hold the LdC fixed
500.0
RES 1 144
END
END

with ntr=1
 during md simulation run.
3. is it required that the protein have to be neutralize during preparation
of parm and topology file by adding ions in explicit solvent methods

4. is it possible that we can simple use the Born GB implicite method to
find salt bridge and analyse the rotamers

regards
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