Folks:
Because of the atom order in Gaussian '03, I'm forced to use ANTE RED in non-automatic mode and select OFF for atom order. The p2n file I get back looks fine. (If I use automatic mode, where H's must follow their attached heavy atoms, the p2n visualization shows a C=O double bond between C5' and O5' in 2'-dA)
When I submit that p2n file and the G'03 output to RED, the p2n visualization again comes back with C=O bond, but I do get charges and the .pdb and .mol2 visualizations show the (expected) H-O and C-O single bonds.
My question is: does it matter that the p2n file I get back from RED shows a C=O? Does that affect the charge calculation? Can I trust the pdb and mol2 files?
Steve
Steven M. Graham. Ph.D.
Associate Professor
Department of Chemistry
St. John's University
8000 Utopia Parkway
Queens, NY 11439
718-990-5217
grahams.stjohns.edu
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Received on Wed Feb 08 2012 - 08:30:02 PST
