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Shya, Elbow command: phenix.elbow --smiles="O=C(C[N+]23CN1CN(CN(C1)C2)C3)c4cccc5ccccc45" will give you CIF and PDB files. I just tried, it took 5 minutes to calculate them on my mac. Pavel On Wed, May 9, 2012 at 9:08 AM, Shya Biswas <[log in to unmask]> 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. > thanks in advance, > shya >