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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
*

*>
*

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Received on Mon Mar 02 2015 - 12:00:03 PST

Date: Mon, 2 Mar 2015 19:34:11 +0000

Dear Jason,

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:

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Received on Mon Mar 02 2015 - 12:00:03 PST

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