From owner-chemistry@ccl.net Sat Oct 13 23:50:00 2012 From: "Eric Bennett ericb],[pobox.com" To: CCL Subject: CCL: Maestro software Message-Id: <-47763-121013232547-4963-Uc3SV6Ky311L5FRce+lt5A###server.ccl.net> X-Original-From: Eric Bennett Content-Transfer-Encoding: 8bit Content-type: text/plain; charset=us-ascii Date: Sat, 13 Oct 2012 23:25:34 -0400 MIME-version: 1.0 (Apple Message framework v1084) Sent to CCL by: Eric Bennett [ericb|a|pobox.com] If the intention is to minimize it directly with Macromodel as Shinaj stated, then using some other minimization method beforehand could actually be counterproductive, although the other protein prep steps are still useful (for example it doesn't necessarily make sense to minimize with OPLS in protein prep if you are going to switch to some other force field in Macromodel). This structure is a nucleic acid with potassium ions. A couple possibly relevant points: (1) Not all of the force fields in Macromodel will have all of the parameters required for this system. (2) The PDB file specifies bonds between oxygen atoms and the potassium ions. Check to make sure the metal ions are free standing; the force fields generally do not accept metals that are input with explicit coordination bonds. Cheers, Eric On Oct 13, 2012, at 10:37 AM, David Watson dewatson^^go.olemiss.edu wrote: > > Sent to CCL by: David Watson [dewatson_._go.olemiss.edu] > Many of the protein structures in the PDB are missing atoms, residues, etc. > In fact, you can bet that crystal structures (as opposed to NMR) for macromolecules will not have any hydrogens assigned. > If you are using Maestro, then you need to use the Protein Preparation Wizard to import the PDB file, generate atom types, add hydrogens, assign bond orders, etc. > One very important consideration before running any of the other Schrodinger utilities is to use the constrained minimization process in the Protein Preparation Wizard before using any of the other Schrodinger applications. > > Best of luck > > On Oct 13, 2012, at 12:38 AM, Shinaj Rajagopal K shinaj[-]iisertvm.ac.in wrote: > >> >> Sent to CCL by: "Shinaj Rajagopal K" [shinaj/a\iisertvm.ac.in] >> I was trying to minimize the structure of a G-quadruplex structure which i >> downloaded from the PDB bank. But while i was running for the minimization >> using MacroModel with Schrodinger software Maestro 9.1, error generating >> interactions, aborted the minimization of the structure. >> The crytal structure(PDB code: 1KF1)was downloaded as pdb file and was put in >> the Maestro software for getting the minimized structure. >> >> Is the integrity of the structure lost while i download the file from data >> bank? If so can anyone suggest me how to download in a proper way from the PDB >> bank, since these structures are minimized and uploaded to the data bank. >> >> >> >