On 11/10/17 11:59 PM, Ahmet Yildirim wrote:
Hi,
Just tested it. The [ dihedral_restraints ] didn't help. The RMSD of the
ligand is the same when the [ dihedral_restraints ] or [ dihedrals ] is
used at end of the complex topology file. This is a bug?
I doubt there's a bug. I tested this feature a lot myself and have used
it. How different are the dihedrals in the B-state vs. the A-state, and
how much do they differ from the target values? Note that choosing
appropriate atoms to apply restraints is not a trivial matter, and
results can vary depending on the choices made.
-Justin
From my first mail:
I think [ dihedral_restraints ] will be the same as [ dihedrals ] because
the eq. 4.84 in the manual will be equal to 4.61 if dphiA and dphiB are
taken as 0 (zero), right?
Checked also the position of the ligand during the simulation on the VMD.
It is very mobile in the decoupled state as I said in the previous mail.
*First test:*
[ intermolecular_interactions ]
[ bonds ]
; ai aj type bA kA bB kB
1391 2615 6 0.654 0.0 0.654 4184.0
[ angles ]
; ai aj ak type thA fcA thB fcB
1393 1391 2615 1 88.8 0.0 88.8 41.84
1391 2615 2614 1 32.9 0.0 32.9 41.84
[ dihedrals ]
; ai aj ak al type thA fcA thB fcB
1410 1393 1391 2615 2 -159.7 0.0 -159.7 41.84
1393 1391 2615 2614 2 122.6 0.0 122.6 41.84
1391 2615 2614 2610 2 12.8 0.0 12.8 41.84
*Second test:*
[ intermolecular_interactions ]
[ bonds ]
; ai aj type bA kA bB kB
1391 2615 6 0.654 0.0 0.654 4184.0
[ angles ]
; ai aj ak type thA fcA thB fcB
1393 1391 2615 1 88.8 0.0 88.8 41.84
1391 2615 2614 1 32.9 0.0 32.9 41.84
[ dihedral_restraints ]
; ai aj ak al type phiA dphiA fcA phiB dphiB
fcB
1410 1393 1391 2615 1 -159.7 0.0 0.0 -159.7 0.0
41.84
1393 1391 2615 2614 1 122.6 0.0 0.0 122.6 0.0
41.84
1393 1391 2615 2614 1 12.8 0.0 0.0 12.8 0.0
41.84
On 10 November 2017 at 22:36, Justin Lemkul <jalem...@vt.edu> wrote:
On 11/10/17 2:21 PM, Ahmet Yildirim wrote:
Dear users,
I add the following [ intermolecular_interactions ] section into the
topology file of protein-ligand complex for free energy calculations.
Unfortunately this setting doesn't provide me what I want in the decoupled
state. The ligand in the decoupled state is very mobile compared to the
coupled state. It means that the conformational sampling of the ligand in
the decoupled state is quite different from the coupled state. That is not
expected of course. Any suggestions as to why this might be?
Do you think that there is something wrong with the following settings,
e.g. [ dihedrals ] part?
Yes, because you're setting [dihedrals] as if they were restraints.
Dihedrals have a multiplicity, phase angle (not the angle you want it to
be, it's the shape and position of the minima in the function) and a force
constant. So mdrun is doing what you're telling it, but what you're telling
it doesn't make physical sense.
[ intermolecular_interactions ]
[ bonds ]
; ai aj type bA kA bB kB
1391 2615 6 0.654 0.0 0.654 4184.0
[ angles ]
; ai aj ak type thA fcA thB fcB
1393 1391 2615 1 88.8 0.0 88.8 41.84
1391 2615 2614 1 32.9 0.0 32.9 41.84
[ dihedrals ]
; ai aj ak al type thA fcA thB fcB
1410 1393 1391 2615 2 -159.7 0.0 -159.7 41.84
1393 1391 2615 2614 2 122.6 0.0 122.6 41.84
1391 2615 2614 2610 2 12.8 0.0 12.8 41.84
Should I use the following [ dihedral_restraints ] part instead of the
above [ dihedrals ] part?
Yes, this would probably accomplish what you want.
-Justin
[ dihedral_restraints ]
; ai aj ak al type phiA dphiA fcA phiB dphiB
fcB
1410 1393 1391 2615 1 -159.7 0.0 0.0 -159.7 0.0
41.84
1393 1391 2615 2614 1 122.6 0.0 0.0 122.6 0.0
41.84
1393 1391 2615 2614 1 12.8 0.0 0.0 12.8 0.0
41.84
I think [ dihedral_restraints ] will be the same as [ dihedrals ] because
the eq. 4.84 in the manual will be equal to 4.61 if dphiA and dphiB are
taken as 0 (zero), right?
Thanks in advance
--
==================================================
Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry
303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061
jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
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==================================================
Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry
303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061
jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
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