thank u very much again!
the problem is that the vina output is also stripped from the hydrogen ( i
don’t know why because I've made each ligand including hydrogens from the
initial.pdb where they were)
pythonsh ${tools}/prepare_ligand4.py -v -l ${mol2} -o
${ligands_out}/${filenamenoextention_lig
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. https://code.google.com/p/acpy
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 amber
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 S
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
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
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 tutorial
