On 13/02/2011 5:03 PM, TJ Mustard wrote:
On February 12, 2011 at 9:31 PM Mark Abraham <[email protected]>
wrote:
On 13/02/2011 3:57 PM, TJ Mustard wrote:
On February 12, 2011 at 5:35 PM Mark Abraham
<[email protected]> <mailto:[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.
Well my major problem is the energy being transmitted about 12
angstroms away into my FEP molecule. I have consistently gotten an
interaction energy of around ~130 kJ/mol. With these restraints on the
energy spikes to ~125000 kJ/mol. Since I have my rvdw, rcoulomb, rlist
being 1.0 (nm), do I need to move these constraints father away from
the ligand?
Hence my thinking that you're somehow applying restraints to the wrong
[moleculetype] and the FEP is amplifying the problem. Can you run normal
MD normally, with and without restraints?
Mark
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.
I have just looked into this and I will hopefully be able to use this
for the other projects I have.
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.
Well I will stay away from this for now then.
Thank you,
TJ Mustard
Mark
TJ Mustard
Email: [email protected]
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