HI - try the program contact from the ccp4 suite.
http://www.ccp4.ac.uk/html/contact.html
J
Eleanor Dodson <[EMAIL PROTECTED]> wrote:>
> mathias wrote:
>> Dear all,
>>
>> Can anyone of you guys recommend free software, or any open access
>> internet server, to calculate VDW interactions of smal
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
int
AIL.AC.UK
cc
Subject
[ccp4bb] software to calculate VDW interactions between small molecule and
protein
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 nee
Hi Mattias,
CCP4mg will list contact areas in the form of the attached file.
This is evaluating the buried area (ie difference is solvent accessible area
with and without the ligand bound).
It ought to be possible to run a script if you have a significant number of
structures - contact me for
Molprobity has a great tool for this under the section Visualize
interface contacts. One caveat though, if the small molecule isn't
already in ligand depot you have to provide your own PDB format
description.
On 2/27/07, mathias <[EMAIL PROTECTED]> wrote:
Dear all,
Can anyone of you guys reco
Dear Mathias,
In the old days, I used a program called "ligplot", which gives you
a .ps output file with the interactions involved, and the distances.
I'm using PyMol as well, but things might not be exactly what you
want. Here, I'm just looking at residues 4.2 angstrom away in the
intera
iginal Message-
From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of mathias
Sent: Tuesday, February 27, 2007 10:44 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] software to calculate VDW interactions between small molecule
and protein
Dear all,
Can anyone of you guys recommend fre
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 wi
