On 11/13/17 3:00 AM, Ahmet Yildirim wrote:
Sorry. The pymol and GROMACS give the same results for every three target
dihedrals. The updated results are here:
https://www.dropbox.com/s/7qgn7qa4rf2yc14/dih.pdf?dl=0
The results show that the average dihedrals are almost the same in both the
state A and state B for both [dihedrals] or [dihedral_restraints]. I think
this is normal?
Yes, because the purpose of selectively turning on the additional bond
or restraint potential is to enforce the original geometry. Your results
look fine to me, probably you just need a slightly larger force constant.
-Justin
On 13 November 2017 at 09:49, Ahmet Yildirim <ahmedo...@gmail.com> wrote:
Hi,
Let me take that in reverse order:
Note that choosing appropriate atoms to apply restraints is not a trivial
matter, and results can vary depending on the choices made.
I know.
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?
The dihedrals are almost the same in both the state A and state B (except
for the first one) when the [dihedrals] or [dihedral_restraints] is used.
Please see the results https://www.dropbox.com/s/rdw6
lg0c4xviufk/dih.pdf?dl=0
I think there is bug?
On the other hand, the pymol and GROMACS calculate differently the first
target dihedral angle between 1587, 1581, 1579 and 14 atoms, respectively
-155 and 66. I don't know why? That is strange? Note that I used -155
degrees obtained from pymol as a target value of the first dihedral in the
simulation. The other two target dihedrals are the same for both pymol and
GROMACS.
Thanks.
On 13 November 2017 at 01:55, Justin Lemkul <jalem...@vt.edu> wrote:
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
<https://maps.google.com/?q=the+eq.+4.84+in+the+manual+will+be+equal&entry=gmail&source=g>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
==================================================
--
Gromacs Users mailing list
* Please search the archive at http://www.gromacs.org/Support
/Mailing_Lists/GMX-Users_List before posting!
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
send a mail to gmx-users-requ...@gromacs.org.
--
==================================================
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
==================================================
--
Gromacs Users mailing list
* Please search the archive at http://www.gromacs.org/Support
/Mailing_Lists/GMX-Users_List before posting!
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
send a mail to gmx-users-requ...@gromacs.org.
--
Ahmet Yildirim
--
==================================================
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
==================================================
--
Gromacs Users mailing list
* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a
mail to gmx-users-requ...@gromacs.org.
