Dear Jason and David
Thanks for reply, I think updated force fields (like ff10) are not implemented in other dynamics programs. Using NMR restraints option seems ok though tiring.
I have two queries:
I have read amber tutorial: http://ambermd.org/tutorials/advanced/tutorial4/
1) For distance restraints only the non-bonded atoms need to be considered ? I think no need to consider bonded atoms. To make work little easier can I get non-bonded atom distances by some command in amber?
2) As I am not heating to higher temperatures can I skip to provide angle restraints? Or I need to try and see? Similarly any command that can print angles (torsions) in my molecule.
Thanks
kind regards
Jiomm
On Tuesday, November 26, 2013 10:56 PM, case <case.biomaps.rutgers.edu> wrote:
On Tue, Nov 26, 2013, Jio M wrote:
>
> I have three linear polymers and I have placed them parallel to each
> other. I am not sure they have been placed 'very close' because my
> script just considered the atoms as point coordinates while placing
> them. So when I run a simulation they are repelled to each other in
> just 50 ps and the internal geometry of each polymer chain is destroyed
> badly.
> What I am thinking is to run first some simulation considering three
> polymer chains as 'hard rods', that is keeping internal geometry
> coordinates of a polymer constrained (all atoms in a polymer chain being
> fixed with respect to each other; keeping internal geometry of polymer
> chain fixed) so that they just act as hard rods and can adjust their
> positions and later I release the restraints.
You can carry out a version of this sort of calculation using "EMAP"
constraints, as explained in section 6.13 of the manual.� This is not exactly
what you describe, but it might suffice.� You'll probably have to experiment a
bit (or a lot!) with force constants and the resolution of the maps you are
using.� Some other dynamics programs do a better job of allowing you to define
rigid groups that can move relative to each other.
...dac
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Nov 26 2013 - 19:30:02 PST
