Dear Pymol users,
I've decide to make a copy of this topic from the amber mail list because
this problem could be solves by ones of the methods implemented in Pymol.
Here I'm facing with the problem of the preparation of protein-ligand
complexes for amber md simulation:
Following amber's
Hello James,
You can use the Pair Fitting wizard (Menu: Wizards=Pair Fitting) or the
pair_fit command to superimpose small molecules. It's not as
straightforward as protein super/align, since you have to define the atom
pairs that will be superimposed, but it's fairly easy. After that, just
make a
Are there plans to support 4-letter chain IDs, as defined by the current
xPDB/mmCIF specification?
-Spencer
On Tue, Sep 16, 2014 at 3:36 PM, Thomas Holder
thomas.hol...@schrodinger.com wrote:
Hi Folmer and Yeping,
to support upper and lower case letters, set this setting:
PyMOL set
Hi Fotis,
thank you very much for the suggestion!
Indeed I have not had such problem with the preparation structure for NAMD
but in case of amber its really exist (the structure of the ligand provided
in the complex with the receptor.pdb must be EXACTLY the same as it was
previously parametrized
Hi James,
what usually worked for me was simply to do it manually, in editing mode
with pymol.
Consider that you will perform an energy minimization after, so a few
1/10 of angstroms of difference in your initial model are not a big
deal, in my opinion.
Cheers,
Gian
On 9/17/14 3:17 PM, James
all manual and GUI operations are not accepted here!
I'm dealing with the a huge number of protein-ligand complexes (many many
different proteins but only 1 ligand- so the situation is not very bad !).
But what is bad that I need to dock each complex using vina and make its
parametrization by
Hello PyMol users
Is there a way to launch PyMol on the iPad [from another application]
specifying additional parameters, e.g. a pdb code so that the app picks up the
RCSB's PDB and takes you straight to the view?
E.g. .is there a custom URL scheme in use, like pymol://?PDB= that would
Sorry, I didn't get this important point.
Have you tried to run antechamber using your vina output as an input?
You could do something like
grep HETATM output.pdbqt | cut -c1-66 output.pdb
and use acpype to prepare the topology, with output.pdb as an input
file.
Hi Spencer,
multi-letter chain IDs of arbitrary length will be available in the next PyMOL
version. It's in fact already available with the latest updates in our
open-source SVN repository on sourceforge.
Cheers,
Thomas
On 17 Sep 2014, at 06:36, Spencer Bliven sbli...@ucsd.edu wrote:
Are
