Phil

You have a few choices and I'm happy to discuss in detail but the two main choices are

1. Use a SMILES string for each molecule.

2. Use REEL to edit the molecule and run eLBOW directly.

In both cases, you can fit the molecule to your model using GLR.

Sorry for the short answer but I can easily help you directly.

Nigel

On Thu, Apr 25, 2013 at 1:01 PM, Phil Jeffrey <pjeffrey@princeton.edu> wrote:

I've got homologues of small molecule compounds I want to generate restraints for. The changes I'm looking at are converting O to S and moving a substituent around on a phenyl ring. I expect them to have similar conformations overall.

Is the best method to:

1. create a new PDB file of the homolog, change atom types and do some primitive modeling, assuming that the --opt method will fix geometry snafus

~or~

2. use a SMILES string, edit the numbering of the PDB file and regenerate the restraints from that

Thanks
Phil Jeffrey
Princeton
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Nigel W. Moriarty
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