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From: newamber list <newamberlist.gmail.com>

Date: Mon, 2 Mar 2015 18:07:47 +0000

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).

This is very simple problem but am not able to come up with a solution.

Also a mathematical explanation would help.

kind regards,

JIom

_______________________________________________

AMBER mailing list

AMBER.ambermd.org

http://lists.ambermd.org/mailman/listinfo/amber

Received on Mon Mar 02 2015 - 10:30:03 PST

Date: Mon, 2 Mar 2015 18:07:47 +0000

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).

This is very simple problem but am not able to come up with a solution.

Also a mathematical explanation would help.

kind regards,

JIom

_______________________________________________

AMBER mailing list

AMBER.ambermd.org

http://lists.ambermd.org/mailman/listinfo/amber

Received on Mon Mar 02 2015 - 10:30:03 PST

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