Dear Paolo, Is it possible to add also the option to freeze certain internal coordinates (I am particularly interested in freezing the dihedral angles)? Best wishes, Michal
On 26 November 2013 18:09, Paolo Tosco <paolo.to...@unito.it> wrote: > Dear James, > > I will try to get it done during the weekend - I'll get back to you once > it's ready. > > Best, > Paolo > > > > On 11/26/2013 05:51 PM, James Davidson wrote: > > Dear All, > > > > I think this is probably one for Paolo – I was looking at fixing certain > atoms during MMFF minimisation, but couldn’t find the option… Then I > re-read the UGM slides, and found the one titled “Force-field wish list”, > and “fixed atoms” were one of the listed items! > > > > My intended use-case is the following: > > > > 1. Load protein-ligand complex into PyMOL > > 2. Make some changes to the bound ligand (using the Builder > functionality) > > 3. Select atoms that are allowed to move (manual selection, then use > of PyMOL’s ‘flag’ command) > > 4. Pass the molecule over to RDKit (already incorporated in a plugin > we use), to minimise and then pass back (either as a new object, or apply > the new coordinates to the existing object in situ) > > > > Actually, this process is already well-used by some of our chemists here – > as a way of doing some simple modelling / idea exploration – but is > currently using a much ‘flakier’ MMFF implementation. So I would definitely > like to move to RDKit for the minimisation – any idea when a ‘fixed atoms’ > option is likely to be added? > > > > Kind regards > > > > James > > > ______________________________________________________________________ > PLEASE READ: This email is confidential and may be privileged. It is > intended for the named addressee(s) only and access to it by anyone else is > unauthorised. If you are not an addressee, any disclosure or copying of the > contents of this email or any action taken (or not taken) in reliance on it > is unauthorised and may be unlawful. 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