AMBER Archive (2008)

Subject: Re: AMBER: flexible molecule parameterization

From: FyD (
Date: Sun Jan 27 2008 - 08:09:37 CST

Quoting Zhenwei Lu <>:

> I have one flexible ligand which contains negative charge and multiple
> hydroxyl group and tried to do parameterization following the amber
> protocol. First use HF/6-31G* to optimize the structure from PDB and
> then derive the charge. One thing bothers me that two intra-hydrogen
> bonds were formed after optimization. The distance between donor and
> acceptor is 3.5 Angstrom and 2.5 in the optimized structure. I think it
> will always go this way since there is no protein environment. On the
> other hand, I think the parameter should be the similar for the same
> ligand no matter where it is (In the water box or buried in the
> protein). Here is my question: what should I do to get the “right”
> parameter and what’s the effects if I use the one derived from my
> optimized structure? Is it OK to fix all the heavy atoms to do
> optimization? Or is there some protocol for this kind of situation? Any
> suggestion will be appreciated. Zhenwei Lu

Your problem is a difficult one. To solve this problem you might use
dihedral constraint(s) to fix dihedral(s) to a value "you prefer".
However, in this case I always check the frequencies since dihedral
constraint(s) often generate a TS structure.

As an example, you might look at the R.E.DD.B. project "F-60" where RNA nucleosides
were partially optimized using 2 dihedral constraints (to avoid a
canonical hydrogen bond) while DNA nucleosides were fully optimized
(without constraint).

It is written in the "F-60" abstract:
"4 RNA nucleosides [Adenosine, Cytidine, Guanosine and Uridine
(conformation C3'endo, dihedral constraints were used in the geometry
optimization step to avoid intra-molecular hydrogen bonds and
transition state type structures: HO3'-O3'-C3'-C4' = 180 deg.,
HO2'-O2'-C2'-C3' = 290 deg.; 6 mol. orientations)"

regards, Francois

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