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Re: [ccp4bb] software to calculate VDW interactions between small molecule and protein
 

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CCP4bb <-- 2007 <-- March 2007 <-- 01 March 2007
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Subject: FW: Vacancy in Small Angle Neutron Scattering at ILL, Grenoble.
From: timmins {- at -} ILL {- dot -} FR
Date: 2007-03-01 		Next message:
Subject: Re: R-free error in highest resolution bin
From: ccp4 {- at -} YSBL {- dot -} YORK {- dot -} AC {- dot -} UK
Date: 2007-03-01


Subject: Re: software to calculate VDW interactions between small molecule and protein
From: xgrcri {- at -} IBMB {- dot -} CSIC {- dot -} ES
Date: 2007-03-01
I have had some problems with the PISA server. It is actually very user
fiendly and you
just need a PDB to be uploaded.
The interaction surface renders a value that is in accordance with what
you get with CNS (divided by two),
but when you look at the list of interactions and compare them with the
contacts output of CNS (a then
go back to the display), you find weird things...
The last one was a salt bridge between two main-chain atoms...

Summarising: although it is more tedious, I would reommend CNS. You'll
have to go through the list of contacts below
(say) 4Å by yourself to identify HBs, SBs, and VDWs, but these are
really there...

Eleanor Dodson wrote:

> mathias wrote:
>
>> Dear all,
>>
>> Can anyone of you guys recommend free software, or any open access
>> internet server, to calculate VDW interactions of small molecules
>> binding to protein. The only information I need is an output file
>> which lists all amino acids of the target protein which make VDW
>> interactions with the binding small molecule.
>> Thank you very much for your help and recommendations,
>>
>> Mathias
>>
>>
> Have you tried the MSD Pisa server at the EBI ? It lists all sorts of
> information?
>
> Eleanor
>

--

CCP4bb navigation

CCP4bb <-- 2007 <-- March 2007 <-- 01 March 2007
Previous message:
Subject: FW: Vacancy in Small Angle Neutron Scattering at ILL, Grenoble.
From: timmins {- at -} ILL {- dot -} FR
Date: 2007-03-01 		Next message:
Subject: Re: R-free error in highest resolution bin
From: ccp4 {- at -} YSBL {- dot -} YORK {- dot -} AC {- dot -} UK
Date: 2007-03-01


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