AMBER Archive (2006)

Subject: Re: AMBER: problem in saving parameter file for non-standard residue

From: Priti Hansia (
Date: Fri Jan 13 2006 - 05:50:36 CST

Dear Ilyas,

Thank you again for your reply. I will go through the literature and try
to see if there is any similar structure. I hope I get something !

Thanks again for your help.


> Dear Priti,
> This is a very hard subject; how to find/define the missing parameters.
> You may find a similar structure in literature, or in AMBER, which is
> similar to your non-standart residue, and then assume that the equilibrium
> bond lengths, angles, the force constants, etc., are same as the similar
> structure. Other than that, the hardest way is to calculate the missing
> parameters, which needs x-ray structure, MD simulations, etc. I would
> suggest u to first scan the literature and see if there is any similar
> structure. If yes, use those parameters in your structure. Good luck...

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