Hi Snoze, I'm going to guess, like Elaine, that your purpose is to add partial charges. If your 1000 compounds are in one big mol2 file, here is a script that would do the job: from chimera import openModels, Molecule from AddCharge import addNonstandardResCharges, estimateFormalCharge, ChargeError mols = openModels.list(modelTypes=[Molecule]) log = open("errlog", "w") for m in mols: residues = m.residues atoms = [a for r in residues for a in r.atoms] fc = estimateFormalCharge(atoms) try: addNonstandardResCharges(m.residues, fc) except ChargeError: print>>log, "Charge estimate (%d) or protonation wrong for %s (%s)" % ( fc, m.name, m.oslIdent()) from WriteMol2 import writeMol2 writeMol2(mols, "output.mol2") log.close() If you save the above in a file named script.py and your 1000 compounds are in a file named input.mol2, then running: chimera --nogui input.mol2 script.py will produce a file named output.mol2 with the charges included. Any problems it had charging particular compounds will be saved in a file named errlog. --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu On Feb 1, 2008, at 10:36 AM, Elaine Meng wrote:
Hi Snoze, One of the main uses of the ZINC database is to generate ligand sets for DOCK; I believe you can download mol2 format directly from ZINC, and that the molecules already have hydrogens and charges. See http://zinc.docking.org/
But maybe you wanted to use Antechamber inside of Chimera to get different charges. If so, somebody else will have to answer the scripting part of your question! Best Elaine ----- Elaine C. Meng, Ph.D. meng@cgl.ucsf.edu UCSF Computer Graphics Lab and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html
On Feb 1, 2008, at 9:47 AM, snoze pa wrote:
Dear Chimera Users, How can I use chimera in --nogui mode to screen 1000 compunds from ZINC database and save them in to mol2 format. Is there any script so that I can convert preselected 1000 compound from ZINC database and convert them t o mol2 format so that I can use them in DOCK program. thanks in advance
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