CCL: Maestro software

 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
 <owner-chemistry : ccl.net> 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.
 >>
 >>
 >>
 >