[PyMOL] preparation of protein ligand complexes for the MD simulation

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

Re: [PyMOL] preparation of protein ligand complexes for the MD simulation

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

Re: [PyMOL] naming of chain id

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

Re: [PyMOL] preparation of protein ligand complexes for the MD simulation

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

Re: [PyMOL] preparation of protein ligand complexes for the MD simulation

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

Re: [PyMOL] preparation of protein ligand complexes for the MD simulation

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

[PyMOL] Pymol for iPad: is a custom URL scheme in use?

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 per

Re: [PyMOL] preparation of protein ligand complexes for the MD simulation

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

Re: [PyMOL] preparation of protein ligand complexes for the MD simulation

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

[PyMOL] List

Could you please take my email off the PyMOL user list. Thanks, Everly FLEISCHER Sent from my iPad -- Want excitement? Manually upgrade your production database. When you want reliability, choose Perforce Perforce vers

Re: [PyMOL] naming of chain id

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 wrote: > Are there plans to s

Re: [PyMOL] Pymol for iPad: is a custom URL scheme in use?

Currently right now Mobile PyMOL can be launched using file associations and URLs from any application that supports it (i.e., with file extensions pse, psw, sdf, mol2, mol, pdb) We are in the process of releasing a new version of Mobile PyMOL with minor fixes and updates to support the newer