Hi Rasha,
It will be difficult to specifically set the orientation of hydrogen bonds using Amber programs. One possible way, which I haven't verified, would be to use leap's "impose" command. Another way would be to specify week NMR constraints in the sander input file. An third option, that would be partially outside of Amber, would be to construct the glycans using leap (to get the right atom and residue naming); then open it in a separate external program that can modify internal coordinates and preserve atom and residue names.
Then if you perform Anber MM maximization, the artificial structure you created will be largely conformationally preserved and the internal coordinates will be minimized. However, if you perform unrestrained MD simulations at room or biological temperatures, then all of the intermolecular hydrogen bonds will change and adopt a distribution of conformations and populations. But at least you will have a reasonable input structure.
Cheers,
Karl
----- Original Message -----
From: "Rasha Alqus" <rasha.alqus.manchester.ac.uk>
To: amber.ambermd.org
Sent: Thursday, June 13, 2013 11:26:22 AM
Subject: [AMBER] glycame06_carbohydrate_hydrogen bond pattern
Dear Amber users
my system is formed from chains of carbohydarate, the chains are connected togather by hydrogen bond, a recent paper have published two type of hydrogen bond pattern present for the system. I have built my system but i would like to know how i can set the hydrogen bond between the chains.
Am using Amber12 and GLYCAM06 force field
Thank you
Regards
Rasha
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Received on Thu Jun 13 2013 - 04:30:03 PDT
