Hi Paul The pdb file that you send me does not have the right geometry, have tried phenix elbow, same problem not the right geometry however in consultation with Nigel it looks like a special symbol had to be inserted in smiles, he send me a file that looks like correct. thanks to all who helped, Shya
On Wed, May 9, 2012 at 12:55 PM, Paul Emsley <[email protected]>wrote: > On 09/05/12 17:08, Shya Biswas wrote: > >> Hi all, >> I am having trouble generating a pdb and cif file from the following >> smiles string: >> O=C(C[N+]23CN1CN(CN(C1)C2)C3)**c4cccc5ccccc45 >> >> Prodrg fails to run when i draw the molecule in JME editor was wondering >> if anyone knows a better program which does this kind of job. >> > > I believe that this is supposed to work: > > cprodrg XYZIN mol.smi XYZOUT mol.pdb LIBOUT mol.cif << ! > MINI PREP > END > ! > > (it went boom when I tried it though - but perhaps you can compile it > better - or otherwise make it work. I should add, for balance, that I use > MDL molfiles with cprodrg and they work considerably more robustly). > > Paul. >
