Re: [AMBER] using internal geometry

From: newamber list <newamberlist.gmail.com>
Date: Mon, 2 Mar 2015 19:34:11 +0000

Dear Jason,

>> Do you have the internal geometry representation for that residue and you
>> just want to "fill in" the missing atom from that template?

Yes exactly. Thanks for the mathematical explanation. I need to work on
this now.

best regards,
JIom

On Mon, Mar 2, 2015 at 6:35 PM, Jason Swails <jason.swails.gmail.com> wrote:

> On Mon, Mar 2, 2015 at 1:07 PM, newamber list <newamberlist.gmail.com>
> wrote:
>
> > Dear All,
> >
> > I am sure this is irrelevant question for AMBER but tleap functionality
> in
> > AMBERTools does this job. For example if there is any missing atom in the
> > loaded pdb then tleap can add that missing atom using residue library.
> >
> > I think this tleap module uses internal geometry (Z matrix) of the
> residue
> > and generates a new Cartesian coordinate in space for missing atom. I
> have
> > similar problem which I tried to ask in babel community but no reply.
> >
> > Lets say I have a,b,c,d four atoms (or even more). I can use babel to
> > generate Z matrix which is internal geometry coordinates. I have many
> cases
> > when I need to find Cartesian coordinate of atom 'a' given that I know
> > Cartesian coordinate for b,c and d (other atoms too).
> >
>
> ​Do you have the internal geometry representation for that residue and you
> just want to "fill in" the missing atom from that template?
> ​
>
> > This is very simple problem but am not able to come up with a solution.
> > Also a mathematical explanation would help.
> >
>
> ​Basically what the process boils down to is generating a system of
> equations to solve for the x, y, and z coordinates of the missing atom (a)
> by creating 3 equations (since you have 3 unknowns). If you know the
> positions of ​
> 3 atoms (b, c, d) and the b-a bond, a-b-c angle, and a-b-c-d torsion
> angles, then you can create 3 equations by computing the distance, angle,
> and dihedral expressions and solving for xa, ya, and za. Of course, this
> *assumes* that you know the internal coordinate representation (e.g., from
> the template).
>
> Another way mathematicians often frame this type of problem is to use a
> 'coordinate system' that is convenient for your problem (in your case, a
> set of internal coordinates) and then using the Jacobian to translate
> between the two different coordinate systems.​
> ​
>
> HTH,
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Mar 02 2015 - 12:00:03 PST
Custom Search