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Hello Martin-- > thanks for your reply. Yes that's more or less what we've done here in our > modified peptides and unnatural residues work. As you say, it's mostly by > hand and doable, just not optimal. We here certainly haven't tried to do a > complete small molecule this way, just things like oxazole/thoazole modified > peptide backbones etc., all our lactam bridge stuff can be accommodated with > normal patches etc. But for small organic molecules, what we really are > waiting for is an atom-based forcefield not residue-based so that if you can > draw it, minimise it, and label it then you can xplor it! > In some cases you might be able to use the genLigand tool (eginput/PSF_generation/genLigand.py). This generates PSF and parameter files directly from ATOM or HETATM records in a PDB file. There is a major limitation currently- that the ligand must be treated as a rigid body, as no bond information is generated. I plan on reading CONECT records for this purpose. best regards-- Charles -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.9 (GNU/Linux) Comment: Processed by Mailcrypt 3.5.8+ <http://mailcrypt.sourceforge.net/> iEYEARECAAYFAkp4RHUACgkQPK2zrJwS/la6bQCfRu8HEhopszhe4cSeMxNS2pWv QiMAoIeZErpxaNAVtkH6wOz95L263JZw =QhZB -----END PGP SIGNATURE-----
