AMBER Archive (2003)

Subject: Re: AMBER: double bonds in prmtop

From: Herbert Georg (hcgeorg_at_if.usp.br)
Date: Fri Sep 19 2003 - 16:27:53 CDT

Hi, Ioana

Ok, but my doubt is: if I have a chain like this

C -- C == C -- C

all of them are sp2 carbons but the bonds are different. I could have
likewise

C == C -- C == C

Does amber attribute the same R0 and K_R to the bonds or it recognizes
where are the double bonds. If it recognizes, how does it do it?

Ioana Cozmuta escreveu:

>Hi,
>
>I do not think that information is contained in the PDB file but that's
>why you generate the topology. You read the atom names and AA sequence
>from the PDB file and you know which atom is sp2 or sp3 and you associate
>the right atom type from the force field. The force field then defines
>what constants to use in the potential depending on the atoms involved in
>the same bond, angle, torsion etc.
>
>In the pdb file you have the atoms coordinates but the "equilibrium" bonds
>in the simulation are those defined by the FF.
>
>I assume that's how this works.
>
>Ioana
>
>On Fri, 19 Sep 2003, Herbert Georg wrote:
>
>
>
>>I would like to know how does AMBER treat double bonds. How does it know
>>if a bond is a single or doube or even a triple one? Does it use the
>>bond lenght given, by PDB file for example, as R0 or it uses the lenght
>>given by literature?
>>
>>
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