AMBER Archive (2009)

Subject: Re: [AMBER] Restrained backbone conformation MD simulation"

From: Carlos Simmerling (carlos.simmerling_at_gmail.com)
Date: Fri Jul 10 2009 - 06:47:20 CDT

1. restrained backbone normally means cartesian (ntr=1) restraints.
2. 500 is much too strong for a force constant, 10 should be enough, or even
1. your group input is not right for just the backbone. I suggest using the
restraintmask functino, there are examples in the manual and plenty in the
archives. that way you can easily select specific residue ranges and atom
names.
3. it is not required, but you may want to do this. it really depends on the
system and you will have to use your experience with simulations to help you
decide, or your reading of the literature for simulations that worked well
at solving scientific problems similar to yours.
4. the GB model can work reasonably well, but we and other have shown that
it's ability to describe salt bridges is perhaps one of the weakest parts of
the model. see for example
Okur, A., Wickstrom, L. and Simmerling, C., “*Evaluation of salt bridge
structure and energetics in peptides using explicit, implicit and hybrid
solvation models*”, J. Chem. Theory Comput., 4:288-298 (2008)
Geney, R., Layten, M., Gomperts, R., Hornak, V. and Simmerling, C.,
“*Investigation
of salt bridge stability in a Generalized Born solvent model*”, J. Chem.
Theory Comput., 2:115, 2006.

On Fri, Jul 10, 2009 at 7:27 AM, Prem Prakash Pathak
<prempolymer_at_gmail.com>wrote:

> 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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> AMBER mailing list
> AMBER_at_ambermd.org
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>
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