AMBER Archive (2004)

Subject: RE: AMBER: universal recognition of chemicals

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Mon Apr 26 2004 - 17:35:41 CDT

Dear Ioana,

I suggest you read the Antechamber section of the manual. This is designed
to do what you suggest for common organic (pharmaceutical like) molecules by
making use of the Generalised Amber Force Field (GAFF). Although currently
this will only work with C,N,O,S,P,H,F,Cl,Br and I elements.

I hope this helps.
All the best
Ross

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|\oss Walker

| Department of Molecular Biology TPC15 |
| The Scripps Research Institute |
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> -----Original Message-----
> From: owner-amber_at_scripps.edu
> [mailto:owner-amber_at_scripps.edu] On Behalf Of Ioana Cozmuta
> Sent: 26 April 2004 15:16
> To: Amber List
> Subject: AMBER: universal recognition of chemicals
>
> Hi amber users,
>
> Is there a way to make amber recognize and build
> automatically a topology
> for any given chemical? What would be the limitations?
>
> To my knowledge amber recognizes residues and will not build
> a topology
> file if the structure does not match one that exists in its library.
> Is there a way to shortcut the "residue recognition" and use the atom
> types, bond, angles and torsions defined by default in the
> force field?
>
> Thank you,
> Ioana
>
>
> ******************
> Ioana Cozmuta, PhD
> Research Scientist
> Eloret Corporation
> Mail Stop 230-3
> NASA AMES Research Center
> Moffet Field, CA 94035-1000
> Phone: (650) 604-0993
> http://www.ipt.arc.nasa.gov/computationalpeople.html
>
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