CCL: Maestro software
- From: Eric Bennett <ericb(a)pobox.com>
- Subject: CCL: Maestro software
- Date: Sat, 13 Oct 2012 23:25:34 -0400
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.
>>
>>
>>
>