Re: [Cdk-devel] MMFF94 FF in the CDK

[Rajarshi Guha <rguha@in...>]

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On Jun 15, 2008, at 9:44 AM, Christoph Steinbeck wrote:
> Hi Rajarshi,
>
> The MMFF94 implementation as it is at the moment gives grossly  
> wrong energies. It can simply be considered to be broken.
> This was recently noticed by a colleague here at EBI who is now  
> working on a correct MMFF94 implementation, which already seems to  
> be doing reasonable things.
>
> I'll put you in touch with him, if you like.
> He said, the stuff will of course be released as soon as it has  
> been tested.

Excellent! No hurry - as always, too many things to do. But in the  
medium term I would like to implement some form of molecular field  
code, for which the MMFF94 energies would be a good starting point

- -------------------------------------------------------------------
Rajarshi Guha  <rguha@...>
GPG Fingerprint: D070 5427 CC5B 7938 929C  DD13 66A1 922C 51E7 9E84
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Heisenberg may have slept here...


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[Cdk-devel] MMFF94 FF in the CDK

[Rajarshi Guha <rguha@in...>]

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Hi, can anybody comment on the status of the MMFF94 forcefield in the  
CDK? Specifically I'm interested in getting an energy for a 3D  
structure (no optimization etc) as well as calculating interactin  
energies between atoms. What I'd like to have is something that can  
evaluate molecular fields (ala GRID)

- -------------------------------------------------------------------
Rajarshi Guha  <rguha@...>
GPG Fingerprint: D070 5427 CC5B 7938 929C  DD13 66A1 922C 51E7 9E84
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A method of solution is perfect if we can forsee from the start,
and even prove, that following that method we shall attain our aim.
	-- Leibnitz


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Re: [Cdk-devel] MMFF94 FF in the CDK

[Christoph Steinbeck <steinbeck@eb...>]

Hi Rajarshi,

The MMFF94 implementation as it is at the moment gives grossly wrong 
energies. It can simply be considered to be broken.
This was recently noticed by a colleague here at EBI who is now working 
on a correct MMFF94 implementation, which already seems to be doing 
reasonable things.

I'll put you in touch with him, if you like.
He said, the stuff will of course be released as soon as it has been tested.

Cheers,

Chris



Rajarshi Guha wrote:
> Hi, can anybody comment on the status of the MMFF94 forcefield in the  
> CDK? Specifically I'm interested in getting an energy for a 3D  
> structure (no optimization etc) as well as calculating interactin  
> energies between atoms. What I'd like to have is something that can  
> evaluate molecular fields (ala GRID)
> 
> -------------------------------------------------------------------
> Rajarshi Guha  <rguha@...>
> GPG Fingerprint: D070 5427 CC5B 7938 929C  DD13 66A1 922C 51E7 9E84
> -------------------------------------------------------------------
> A method of solution is perfect if we can forsee from the start,
> and even prove, that following that method we shall attain our aim.
> 	-- Leibnitz
> 
> 

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Dr. Christoph Steinbeck
Head of Chemoinformatics and Metabolism
European Bioinformatics Institute (EBI)
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Phone +44 1223 49 2640

What is man but that lofty spirit - that sense of enterprise.
... Kirk, "I, Mudd," stardate 4513.3..

Re: [Cdk-devel] MMFF94 FF in the CDK

[Rajarshi Guha <rguha@in...>]

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On Jun 15, 2008, at 9:44 AM, Christoph Steinbeck wrote:
> Hi Rajarshi,
>
> The MMFF94 implementation as it is at the moment gives grossly  
> wrong energies. It can simply be considered to be broken.
> This was recently noticed by a colleague here at EBI who is now  
> working on a correct MMFF94 implementation, which already seems to  
> be doing reasonable things.
>
> I'll put you in touch with him, if you like.
> He said, the stuff will of course be released as soon as it has  
> been tested.

Excellent! No hurry - as always, too many things to do. But in the  
medium term I would like to implement some form of molecular field  
code, for which the MMFF94 energies would be a good starting point

- -------------------------------------------------------------------
Rajarshi Guha  <rguha@...>
GPG Fingerprint: D070 5427 CC5B 7938 929C  DD13 66A1 922C 51E7 9E84
- -------------------------------------------------------------------
Heisenberg may have slept here...


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Re: [Cdk-devel] MMFF94 FF in the CDK

[Egon Willighagen <egon.willighagen@gm...>]

On Sun, Jun 15, 2008 at 3:44 PM, Christoph Steinbeck
<steinbeck@...> wrote:
> The MMFF94 implementation as it is at the moment gives grossly wrong
> energies. It can simply be considered to be broken.
> This was recently noticed by a colleague here at EBI who is now working
> on a correct MMFF94 implementation, which already seems to be doing
> reasonable things.

How does the MMFF94 FF compare to the UFF?

> I'll put you in touch with him, if you like.
> He said, the stuff will of course be released as soon as it has been tested.

This is CDK-based? Will it be release as CDK module, with LGPL?

Egon

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