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On 27/02/2012 8:35 PM, James Starlight wrote:
<blockquote
cite="mid:CAALQopw-qrbFQua87LReKa_eH6bHQaw93Obspfcbhqf6Ncu3Eg@mail.gmail.com"
type="cite">Mark,<br>
<br>
I've found a possible sollution to restrict oxygens of my X-ray
water by possible plasing the below string in the TOPOLOGY.top of
my system<br>
<br>
; Include X-ray water topology<br>
#include "XW.itp"<br>
<br>
; Include Position restraint file<br>
#ifdef POSRES_XW<br>
[ position_restraints ]<br>
; i funct fcx fcy fcz<br>
1 1 1000 1000 1000<br>
#endif<br>
<br>
I havent recieved any errors from gromp. Does this aproach correct
in general ?<br>
</blockquote>
<br>
Yes. There's only one heavy atom in a water, so that's all you need
to restrain. You want it to have rotational freedom for EM, of
course.<br>
<br>
<blockquote
cite="mid:CAALQopw-qrbFQua87LReKa_eH6bHQaw93Obspfcbhqf6Ncu3Eg@mail.gmail.com"
type="cite">
<br>
I dont know why but after minimisation constrained mollecules were
diffused from the protein interious so POSRES have not worked :(<br>
</blockquote>
<br>
That's sterically impossible with or without position restraints.
Either you're looking at the wrong before-and-after files, or the
after file has some periodicity artefact in your viewing program. If
you set nstxout = 1 then you can watch the EM process step by step.<br>
<br>
<blockquote
cite="mid:CAALQopw-qrbFQua87LReKa_eH6bHQaw93Obspfcbhqf6Ncu3Eg@mail.gmail.com"
type="cite"><br>
My minim.mdp consist of two separate posres for water as well as
for ligand groups ( there are no posre for protein).<br>
<br>
<br>
define = -DPOSRES_LIG -DPOSRES_XW ; position restrain
the protein<br>
integrator = steep ; Algorithm (steep = steepest descent
minimization)<br>
emtol = 1000.0 ; Stop minimization when the maximum
force < 1000.0 kJ/mol/nm<br>
emstep = 0.01 ; Energy step size<br>
nsteps = 50000 ; Maximum number of (minimization)
steps to perform<br>
energygrps = Protein CAR<br>
<br>
What should I add to that file to activate posres? <br>
Finally are the constraints algorithm needed here ?<br>
<br>
<br>
James<br>
<br>
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<br>
</blockquote>
<br>
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