Dear Michal, internal coordinate constraints are part of the plan - not sure whether I will succeed in adding constraints on both atoms and internals by the end of the week, but I'll try.
Cheers, p. On 11/27/2013 04:41 PM, Michal Krompiec wrote: > 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 <[email protected]> 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. 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