[gmx-users] protein and ligand is not forming complex after completing simulation

[Swagata Patra]

Hi Marlon.
The commands that you gave
trjconv_d -s md_0_1.tpr -f md_0_1.xtc -n index.ndx -o trj0.pdb -pbc nojump

trjconv_d -s md_0_1.tpr -f trj0.xtc -n index.ndx -o trj1.pdb -center [[Here
center on your protein for example]]

trjconv_d -s md_0_1.tpr -f trj1.xtc -n index.ndx -o trj2.pdb -pbc mol

>From where will get trj0.xtc file?

On Wed, Jul 27, 2016 at 7:30 PM, Swagata Patra <swagataliza at gmail.com>
wrote:

> Thank you Marlon for your suggestion. It really helped a lot.
>
> On Wed, Jul 27, 2016 at 7:28 PM, Swagata Patra <swagataliza at gmail.com>
> wrote:
>
>> thank you James and Felipe for your suggestion. It really helped me a
>> lot to understand the situation.
>> I am trying to resolve the problem.
>>
>> On Wed, Jul 27, 2016 at 6:00 PM, Felipe Merino <
>> felipe.merino at mpi-dortmund.mpg.de> wrote:
>>
>>> Hey,
>>>
>>> Of course you can always use VMD, for example, to check several adjacent
>>> copies of the simulation cell in order to see if your problem is PBC or not.
>>>
>>> Felipe
>>>
>>>
>>> On 27/07/16 14:21, Justin Lemkul wrote:
>>>
>>>>
>>>>
>>>> On 7/27/16 8:18 AM, Swagata Patra wrote:
>>>>
>>>>> For trjconv i used the following command:
>>>>>
>>>>> trjconv_d -s md_0_1.tpr -f md_0_1.xtc -n index.ndx -o trj.pdb -pbc mol
>>>>> -ur
>>>>> compact -dt 30000
>>>>>
>>>>>
>>>> The PBC fitting routines sometimes struggle with large -dt. You're
>>>> basically just trying to dump out the final frame, which is redundant with
>>>> what you're doing below.  If you want to obtain a PBC-corrected trajectory,
>>>> follow the link I provided.
>>>>
>>>> For editconf I simply used : editconf_d -f md_0_1.gro -o md_0_1.pdb
>>>>>
>>>>> I have analyzed the H-bonds between protein and ligand, there showing
>>>>> formation of H-bonds.
>>>>>
>>>>> if ligand is dissociating, what could be the reason?
>>>>>
>>>>>
>>>> Bad topology, incorrect run settings, etc.  But from the simple matter
>>>> of disagreement above, I doubt there's actually a problem. Nearly always,
>>>> "dissociation" is just a PBC issue that needs to be handled carefully.
>>>>
>>>> -Justin
>>>>
>>>>
>>>>> On Wed, Jul 27, 2016 at 5:40 PM, <jkrieger at mrc-lmb.cam.ac.uk> wrote:
>>>>>
>>>>> Hi Swagata,
>>>>>>
>>>>>> Perhaps your ligand is dissociating during the simulation. What
>>>>>> frames are
>>>>>> you looking at with trjconv and editconf? If these are different you
>>>>>> may
>>>>>> be seeing bound and unbound snapshots.
>>>>>>
>>>>>> Best wishes
>>>>>> James
>>>>>>
>>>>>> hi everyone,
>>>>>>>
>>>>>>> I  simulated protein-ligand complex for 30ns and then visualize the
>>>>>>> complex
>>>>>>> after simulation in pymol.
>>>>>>>
>>>>>>> I got the .pdb file using two commands from final simulated file.
>>>>>>> One is using trjconv, from .xtc to .pdb. When I am visualizing this
>>>>>>> .pdb
>>>>>>> file, protein and ligand has not formed any complex.
>>>>>>> Another one is using editconf, from .gro to .pdb. When I am
>>>>>>> visualizing
>>>>>>> this .pdb file, protein and ligand  formed  complex.
>>>>>>>
>>>>>>> Why is this happening? Can anyone explain it?
>>>>>>>
>>>>>>> Thanks in advance.
>>>>>>>
>>>>>>> --
>>>>>>> Swagata Patra
>>>>>>> M.Tech (Biotech)
>>>>>>> JRF
>>>>>>> IIT Guwahati
>>>>>>> --
>>>>>>> Gromacs Users mailing list
>>>>>>>
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>>>>>>>
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>>>>>>
>>>>>> --
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>>>>>>
>>>>>
>>>>>
>>>>>
>>>>
>>> --
>>> Felipe Merino
>>> Max Planck Institute for Molecular Physiology
>>> Department of Structural Biochemistry
>>> Otto-Hahn-Str. 11
>>> 44227 Dortmund
>>> Phone: +49 231 133 2315
>>>
>>>
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>>> Gromacs Users mailing list
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>>
>>
>>
>> --
>> Swagata Patra
>> M.Tech (Biotech)
>> JRF
>> IIT Guwahati
>>
>
>
>
> --
> Swagata Patra
> M.Tech (Biotech)
> JRF
> IIT Guwahati
>



-- 
Swagata Patra
M.Tech (Biotech)
JRF
IIT Guwahati