[gmx-users] mobile ligand with intermolecular interactions

[Ahmet Yildirim]

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?
>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 <jalemkul at 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
>
> jalemkul at vt.edu | (540) 231-3129
> http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
>
> ==================================================
>
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-- 
Ahmet Yildirim