On Sun, Nov 27, 2011, jun kit wrote:
> After I analyze my structure with MOE, I found out that it is not
> necessary to add a hydrogen at the "phenol"group. The "phenol" group and
> "amine" group is meant to form a hydrogen bond. So a O at "phenol" group
> will be O- and a N in the "amine" group will be N+.
Make sure then that the overall stoichiometry works out: if you phenol has a
-3 charge and the amine a +1, then be sure there are three amines for every
phenol (assuming there are no other charged species).
>
> 1. Since these both molecules is bonded by hydrogen bond (indeed I need
> this H-bond for study), do I need to derive their charges seperately or
> derive them as a whole?
This is a tough one to answer. You are outside of the comfort range of the
automatic force field programs, so will probably have to do some hand fitting.
If this is a liquid where amine-phenol interactions are being made and broken
periodically, you should probably get a force field for each piece by itself,
but then check that the interaction energy between the two is about what you
want (and modify things if it is not.)
> 2. If I load the structure into antechamber or gaussian, how does the
> program know whether or not my O is negative and my N is positive? The
> -nc flag in antechamber will assign it correctly by automatic?
Quantum chemistry programs need the total charge as input (the -nc variable),
and *you* have to set this -- neither antechamber nor Gaussian will try to
figure that out on its own. Where the charge eventually resides is an output
of the SCF procedure.
> 3. When I load the structure in to LEAP, do I still need to use TER card
> between this "phenol" and "amine" or in between "phenol-amine"?
TER cards come between each individual molecule, i.e. between the phenol and
the amine.
>
> P/S: Sry i am asking too much qyuestion because I am a physics student
> and quite unfamiliar with bonding stuff
You probably need to find a friend who can help you with the "bonding stuff":
I am not familiar with the sorts of systems you are working with.
....dac
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Received on Mon Nov 28 2011 - 10:00:03 PST
