[gmx-users] mobile ligand with intermolecular interactions
Ahmet Yildirim
ahmedo047 at gmail.com
Mon Nov 13 09:00:52 CET 2017
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?
On 13 November 2017 at 09:49, Ahmet Yildirim <ahmedo047 at 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 <jalemkul at 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 <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
>>>>> <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
>>>>
>>>> jalemkul at vt.edu | (540) 231-3129
>>>> http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
>>>>
>>>> ==================================================
>>>>
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>>>> Gromacs Users mailing list
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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
>>
>> jalemkul at vt.edu | (540) 231-3129
>> http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
>>
>> ==================================================
>>
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>> Gromacs Users mailing list
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>> * Please search the archive at http://www.gromacs.org/Support
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>
>
>
> --
> Ahmet Yildirim
>
--
Ahmet Yildirim
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