Hi Julio,
So to be clear here (for my sake!), if the initial PDB complex is
COMPLEX.PDB , I merely extract the ligand say as LIGAND.MOL2, parameterize
it, create the lib, and then invoke that lib in tleap with COMPLEX.PDB ?
COMPLEX.PDB would already contain the ligand, but non-parameterized. This
is what I was asking before (or trying to), does leap simply notice the ID
for the ligand in LIGAND.MOL2, and if that ID appears in COMPLEX.PDB, the
parameters are added/overwritten accordingly?
If this is the case then shouldn't the only change I need to make be in
tleap02.in :
-----------------------------------
source leaprc.ff99SB
source leaprc.gaff
loadamberparams ligand_addH_antechamber.frcmod
loadoff ptb.lib
complex = loadpdb COMPLEX.PDB ************************ #old line was
`complex = loadpdb receptor.pdb`
addions complex Na+ 10
solvatebox complex TIP3PBOX 8.0
saveamberparm complex initial_complex.prm7 initial_complex.rst7
savepdb complex initial_complex.pdb
------------------------------------
And that should load in the receptor+non-parametrized ligand, but
parameterize it from ptb.lib?
Cheers
Sebastian
On 11 April 2013 06:39, Julio Dominguez <acheron24.hotmail.com> wrote:
> Hi Sebastian,
> Since you are using Chimera, I'll use it as a platform to expand on what
> Thomas said. Thomas said that you have to prepare a lib file and still have
> the PDB with receptor an complex. Your original file is the complex, in
> chimera you just need to generate the ligand just by extracting it as you
> mentioned. You use the ligand only to prepare the lib file. After that you
> need the complex+lib file to actually obtain both the receptor and ligand
> for an MD run.
> I usually protonate my ligands in Chimera and then save them as mol2
> files. That has always worked fine for me.
> Best regards.
>
>
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Received on Wed Apr 10 2013 - 20:30:03 PDT
