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On 13/02/2011 3:57 PM, TJ Mustard wrote:
<blockquote
cite="mid:1464589013.18019.1297573073646.JavaMail.open-xchange@oxusgw01.lxa.perfora.net"
type="cite">
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<p style="margin: 0px;"><span>Â </span></p>
<div style="margin: 5px 0px;"> <br>
On February 12, 2011 at 5:35 PM Mark Abraham
<a class="moz-txt-link-rfc2396E" href="mailto:Mark.Abraham@anu.edu.au"><Mark.Abraham@anu.edu.au></a> wrote:<br>
<br>
<blockquote type="cite" style="margin-left: 0px; padding-left:
10px; border-left: 1px solid blue;"> On 13/02/2011 11:49 AM,
TJ Mustard wrote:
<blockquote type="cite">
<p style="margin: 0px;">Hi all,</p>
<p style="margin: 0px;">Â </p>
<p style="margin: 0px;">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?</p>
</blockquote>
<br>
I doubt it.<br>
 <br>
<blockquote type="cite">
<p style="margin: 0px;">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.</p>
<p style="margin: 0px;">Â </p>
<p style="margin: 0px;">Does anyone have an idea what is
happening?</p>
<br>
And if you do, can you please give a recommendation?<br>
</blockquote>
<br>
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. </blockquote>
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<p style="margin: 0px;">Â </p>
<p style="margin: 0px;">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).</p>
</blockquote>
<br>
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.<br>
<br>
<blockquote
cite="mid:1464589013.18019.1297573073646.JavaMail.open-xchange@oxusgw01.lxa.perfora.net"
type="cite">
<p style="margin: 0px;">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.</p>
<br>
; Include Position restraint file<br>
#ifdef POSRES_PROTEIN<br>
#include "posre_Protein_ends_chain_A.itp"<br>
#endif<br>
<br>
<p style="margin: 0px;">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.</p>
<p style="margin: 0px;">Â </p>
<p style="margin: 0px;">[ position_restraints ]<br>
; atom type     fx     fy     fz<br>
    5    1 1000 1000 1000<br>
  262    1 1000 1000 1000</p>
</blockquote>
<br>
Well, that should work, if you put this in the right [moleculetype]
block. Whether that's enough of a restraint can't be said.<br>
<br>
<blockquote
cite="mid:1464589013.18019.1297573073646.JavaMail.open-xchange@oxusgw01.lxa.perfora.net"
type="cite"> <br>
<div style="margin: 5px 0px;">
<blockquote type="cite" style="margin-left: 0px; padding-left:
10px; border-left: 1px solid blue;"> The combination of
g_select and genrestr is probably a more reliable and
documentable way to generate your position restraints.<br>
</blockquote>
</div>
<p style="margin: 0px;">Â </p>
<p style="margin: 0px;">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.</p>
</blockquote>
<br>
I thought you were trying to get all the alpha carbons outside a
sphere, sorry. For just 6 atoms, sure do it by hand.<br>
Â
<blockquote
cite="mid:1464589013.18019.1297573073646.JavaMail.open-xchange@oxusgw01.lxa.perfora.net"
type="cite">
<p style="margin: 0px;">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.</p>
</blockquote>
<br>
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.<br>
Â
<blockquote
cite="mid:1464589013.18019.1297573073646.JavaMail.open-xchange@oxusgw01.lxa.perfora.net"
type="cite">
<p style="margin: 0px;">Would there be a better way to hold these
atoms in the respective locations. I could hold there distances
constant.</p>
</blockquote>
<br>
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.<br>
<br>
Mark<br>
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