On Sat, Nov 04, 2017, jacob wick wrote:
>
> I want to perform a simulation in which I want to set a fixed distance
> between atoms of two different residues.
>
> I have generated 10 unfolded states of a protein and for all of them I want
> to make the distance between C-Alpha atom (residue 2) and N atom(residue
> 64) to be 2.5 while running an MD (initial distances are different in all
> 10 cases). For example, if the distance between C-Alpha atom (residue 2)
> and N atom(residue 64) is 10.6, during simulation I want to decrease the
> distance from 10.6 to 2.5 and then remove the restrains. In Amber 12
> reference manual (p-230) something like this is mentioned with center of
> mass but I could not fix it for my case. I would appreciate any help in
> order to perform such simulations by modifying the md.in file which I have
> as follows:
What you want are called "NMR" restraints in Amber lingo. You would set
nmropt=1, and add an &rst namelist entry for each distance you wish to
restrain.
....hope this helps....dac
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Received on Mon Nov 06 2017 - 01:00:03 PST
