On 13/02/2011 3:57 PM, TJ Mustard wrote:
On February 12, 2011 at 5:35 PM Mark Abraham <[email protected]>
wrote:
On 13/02/2011 11:49 AM, TJ Mustard wrote:
Hi all,
I have been testing the ability of taking a sphere of a protein
around a ligand, and positionally restrain the specified alpha
carbons. I was hoping to keep non connected protein chains from
drifting apart. I have been able to run these md/fep jobs, but I get
huge interaction energies for the ligand, which has no positional
restraints on it. I also don't restrain any atoms within the rvdw,
rcoulomb and rlist radii. Am I thinking this is a possibility when
it is physically impossible to simulate?
I doubt it.
Currently I am selecting all residues around the ligand that have an
atom within 20 Angstroms. I then save this as a pdb file and then
run it through pdb2gmx, manually create a posres.itp file for each
"chain" with their first and last residue's alpha carbon. Once I
turn off these positional restraints the FEP energies drop down to
"normal" levels.
Does anyone have an idea what is happening?
And if you do, can you please give a recommendation?
I'd guess you're not restraining how you think you are :-) Bear in
mind that position restraints are indexed relative to a
[moleculetype] (and must be #included there), and not the whole system.
First I tried setting this globally it the .top file with the
numbering corresponding to the atoms in question there, but found that
the .top file only runs the solvent molecules and all of my reference
atoms were outside the parameters (atoms 1-3 for water).
By default -DPOSRES will only restrain solvent because a) that's all
it's meant to do, because b) that [position_restraints] block is local
to the SOL [moleculetype], like I said.
Then I setup the restraints argument in the Protein_chain_A.itp.itp
file to reference the posre_Protein_ends_chain_A.itp file I made.
; Include Position restraint file
#ifdef POSRES_PROTEIN
#include "posre_Protein_ends_chain_A.itp"
#endif
In the posre_Protein_ends_chain_A.itp file I entered the alpha-C atoms
(2 total both the first residue and last) for the protein.
[ position_restraints ]
; atom type fx fy fz
5 1 1000 1000 1000
262 1 1000 1000 1000
Well, that should work, if you put this in the right [moleculetype]
block. Whether that's enough of a restraint can't be said.
The combination of g_select and genrestr is probably a more reliable
and documentable way to generate your position restraints.
I tried using genrestr directly and found that the selection was
limited to the presets. I then tried to run a make_ndx to select the
residues that were the starting and terminating ends, but I don't know
how and if this program can do this task. I could manually find the
residue numbers and input them directly but knowing that I was looking
to restrain 6 atoms I decided to do it manually.
I thought you were trying to get all the alpha carbons outside a sphere,
sorry. For just 6 atoms, sure do it by hand.
I have yet to look at g_select, as I am just seeing if this idea would
work before I start making a automated script for this.
The point here is that it is straightforward to use g_select to "make an
index group of alpha carbons further than a given distance from some
location" and now you can use genrestr to make position restraints for
that whole group.
Would there be a better way to hold these atoms in the respective
locations. I could hold there distances constant.
Also possible, but (IIRC) the atoms have to be part of the same
[moleculetype], which is awkward for inter-chain restraints. Either way,
you have to address whether your restraints are perturbing the dynamics.
Mark
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