I can send you a complete system prepared in this way containing all
produced files (topologies) and the packmol log. Is it ok ?
I've just made it again with concentration of the solvated ligand 30 and
for the moment everything is ok
Il giorno ven 25 ott 2024 alle ore 15:36 Stephan Schott <
s.schott-verdugo.fz-juelich.de> ha scritto:
> Hi Enrico,
>
> Could you send me an internal link to somewhere I can download your input
> pdbs, params and output? I would need to try to replicate your case.
>
> Best regards,
>
> Stephan Schott Verdugo
> Biochemist
>
>
> Computational Biophysical Chemistry
> Institut für Bio- und Geowissenschaften / Bioinformatik (IBG-4)
> Forschungszentrum Jülich GmbH
> Wilhelm-Johnen-Straße, 52425 Jülich
> Germany
>
>
> ---------------------------------------------------------------------------------------------
>
> ---------------------------------------------------------------------------------------------
> Forschungszentrum Jülich GmbH
> 52425 Jülich
> Sitz der Gesellschaft: Jülich
> Eingetragen im Handelsregister des Amtsgerichts Düren Nr. HR B 3498
> Vorsitzender des Aufsichtsrats: MinDir Stefan Müller
> Geschäftsführung: Prof. Dr. Astrid Lambrecht (Vorsitzende),
> Karsten Beneke (stellv. Vorsitzender), Dr. Ir. Pieter Jansens
>
> ---------------------------------------------------------------------------------------------
>
> ---------------------------------------------------------------------------------------------
>
>
> El vie, 25 oct 2024 a la(s) 2:59 p.m., Enrico Martinez (
> jmsstarlight.gmail.com) escribió:
>
>> No problem Stephan, I manage the thighs!
>>
>> I have a question about the concentration of the added ligand. I am
>> dealing with membrane receptor embedded into membrane contained ligand in
>> binding site that I had used with parametrization without any technical
>> issues.
>>
>> -- When I use the valies from tutorial (--solute_con 4
>> --solute_prot_dist 10) it did not add the ligs to the system but replace
>> all water from the bottom part of the membrane (so the botom part of the
>> system looks empty)
>>
>> -- When I increase it --solute_con 40 --solute_prot_dist 1 it add many
>> ligands in the both parts (above and below the membrane)
>> so how to define the concentration properly e.g. according to
>> experimental data ??
>>
>>
>> Here is the complete packmol command used for this tutorial:
>>
>> packmol-memgen --pdb ./gpcr_lig.pdb --lipids POPC:POPE:POPS --salt_c Na+
>> --ffprot ff14SB --fflip lipid21 --ffwat tip3p --ratio 34:33:33 --keepligs
>> --ligand_param /lig_params/lig.frcmod:/lig_params/lig.lib --notprotonate
>> --nottrim --solute /lig_params/lig.pdb --solute_con 40 --solute_prot_dist 1
>> --parametrize
>>
>> Il giorno ven 25 ott 2024 alle ore 14:12 Stephan Schott <
>> s.schott-verdugo.fz-juelich.de> ha scritto:
>>
>>> Hi Enrico,
>>>
>>> In the manual, page 234 you get an idea what to do.
>>>
>>> Best regards,
>>>
>>> Stephan Schott Verdugo
>>> Biochemist
>>>
>>>
>>> Computational Biophysical Chemistry
>>> Institut für Bio- und Geowissenschaften / Bioinformatik (IBG-4)
>>> Forschungszentrum Jülich GmbH
>>> Wilhelm-Johnen-Straße, 52425 Jülich
>>> Germany
>>>
>>>
>>> ---------------------------------------------------------------------------------------------
>>>
>>> ---------------------------------------------------------------------------------------------
>>> Forschungszentrum Jülich GmbH
>>> 52425 Jülich
>>> Sitz der Gesellschaft: Jülich
>>> Eingetragen im Handelsregister des Amtsgerichts Düren Nr. HR B 3498
>>> Vorsitzender des Aufsichtsrats: MinDir Stefan Müller
>>> Geschäftsführung: Prof. Dr. Astrid Lambrecht (Vorsitzende),
>>> Karsten Beneke (stellv. Vorsitzender), Dr. Ir. Pieter Jansens
>>>
>>> ---------------------------------------------------------------------------------------------
>>>
>>> ---------------------------------------------------------------------------------------------
>>>
>>>
>>> El vie, 25 oct 2024 a la(s) 2:05 p.m., Enrico Martinez (
>>> jmsstarlight.gmail.com) escribió:
>>>
>>>> I gotcha, I am keeping you informed.
>>>>
>>>> Yours with thanks
>>>>
>>>> Enrico
>>>>
>>>> Il giorno ven 25 ott 2024 alle ore 13:18 Elvis Martis <
>>>> elvis.afmartis.gmail.com> ha scritto:
>>>>
>>>>> Hi Enrico
>>>>>
>>>>> To the best of my knowledge both packmol and packmol-memgen should
>>>>> work fine with and without membrane systems.
>>>>>
>>>>> I personally succeeded with packmol when working on systems without
>>>>> membranes.
>>>>>
>>>>> On Friday 25 October 2024, Enrico Martinez <jmsstarlight.gmail.com>
>>>>> wrote:
>>>>>
>>>>>> Dear all,
>>>>>>
>>>>>> thank you very much for these suggestions !
>>>>>>
>>>>>> I am going to check this fantastic option of packmol-memgen. One
>>>>>> question: is it possible to use it exclusively for membrane embedded
>>>>>> protein system or alternatively could it be used for water soluble system
>>>>>> (without the lipids ..) ??
>>>>>>
>>>>>> Many thanks in advance !!
>>>>>>
>>>>>> Enrico
>>>>>>
>>>>>> Il giorno ven 25 ott 2024 alle ore 11:26 Stephan Schott <
>>>>>> s.schott-verdugo.fz-juelich.de> ha scritto:
>>>>>>
>>>>>>> Hi Enrico,
>>>>>>>
>>>>>>> Packmol-memgen can help there as well. This is the tutorial section:
>>>>>>>
>>>>>>> https://ambermd.org/tutorials/advanced/tutorial38/index.php#Ligand_system
>>>>>>>
>>>>>>> Best regards,
>>>>>>>
>>>>>>> Stephan Schott Verdugo
>>>>>>> Biochemist
>>>>>>>
>>>>>>>
>>>>>>> Computational Biophysical Chemistry
>>>>>>> Institut für Bio- und Geowissenschaften / Bioinformatik (IBG-4)
>>>>>>> Forschungszentrum Jülich GmbH
>>>>>>> Wilhelm-Johnen-Straße, 52425 Jülich
>>>>>>> Germany
>>>>>>>
>>>>>>>
>>>>>>> ---------------------------------------------------------------------------------------------
>>>>>>>
>>>>>>> ---------------------------------------------------------------------------------------------
>>>>>>> Forschungszentrum Jülich GmbH
>>>>>>> 52425 Jülich
>>>>>>> Sitz der Gesellschaft: Jülich
>>>>>>> Eingetragen im Handelsregister des Amtsgerichts Düren Nr. HR B 3498
>>>>>>> Vorsitzender des Aufsichtsrats: MinDir Stefan Müller
>>>>>>> Geschäftsführung: Prof. Dr. Astrid Lambrecht (Vorsitzende),
>>>>>>> Karsten Beneke (stellv. Vorsitzender), Dr. Ir. Pieter Jansens
>>>>>>>
>>>>>>> ---------------------------------------------------------------------------------------------
>>>>>>>
>>>>>>> ---------------------------------------------------------------------------------------------
>>>>>>>
>>>>>>>
>>>>>>> El vie, 25 oct 2024 a la(s) 11:22 a.m., Elvis Martis via AMBER (
>>>>>>> amber.ambermd.org) escribió:
>>>>>>>
>>>>>>>> Hi Enrico
>>>>>>>>
>>>>>>>> You could do that using Packmol
>>>>>>>>
>>>>>>>> The following input parameter for Packmol will be helpful
>>>>>>>>
>>>>>>>> structure XXX.pdb >>> PDB for the ligand to be randomly added in
>>>>>>>> the
>>>>>>>> solvent
>>>>>>>> number N
>>>>>>>> inside sphere 0. 0. 0. 50.
>>>>>>>> end structure
>>>>>>>>
>>>>>>>> structure YYY.pdb >>> PDB for protein-ligand complex (ligand in the
>>>>>>>> binding site)
>>>>>>>> number 1
>>>>>>>> inside sphere 0. 0. 0. 50.
>>>>>>>> centerofmass
>>>>>>>> end structure
>>>>>>>>
>>>>>>>> output complex.pdb
>>>>>>>>
>>>>>>>>
>>>>>>>> PS: You could prepare the full complex in packmol and use addtobox
>>>>>>>> in tleap
>>>>>>>> to prepare AMBER prmtop and inpcrd.
>>>>>>>>
>>>>>>>> Hope this helps.
>>>>>>>> Best Regards
>>>>>>>> Elvis
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> On Fri, 25 Oct 2024 at 10:58, Enrico Martinez via AMBER <
>>>>>>>> amber.ambermd.org>
>>>>>>>> wrote:
>>>>>>>>
>>>>>>>> > Dear Amber Users !
>>>>>>>> >
>>>>>>>> > I am working on the protein-ligand system according to amber
>>>>>>>> tutorial. I
>>>>>>>> > was able to prepare the model using parametrization of
>>>>>>>> ante-chamber and
>>>>>>>> > then parametrized the whole complex using tleap. Now I would like
>>>>>>>> to extend
>>>>>>>> > my system, inserting several replicas of the same ligand (present
>>>>>>>> in the
>>>>>>>> > binding pocket, that I parametrized via antechamber) into the
>>>>>>>> solvent to
>>>>>>>> > study it's binding with the protein. How this could be done
>>>>>>>> (replicate
>>>>>>>> > ligand and put it into water of the prepared system or
>>>>>>>> alternatively I need
>>>>>>>> > to prepare it de novo ?) assuming that I have all parameters for
>>>>>>>> this
>>>>>>>> > system ?
>>>>>>>> >
>>>>>>>> > Many thanks in advance
>>>>>>>> >
>>>>>>>> > Enrico
>>>>>>>> > _______________________________________________
>>>>>>>> > AMBER mailing list
>>>>>>>> > AMBER.ambermd.org
>>>>>>>> > http://lists.ambermd.org/mailman/listinfo/amber
>>>>>>>> >
>>>>>>>> _______________________________________________
>>>>>>>> AMBER mailing list
>>>>>>>> AMBER.ambermd.org
>>>>>>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> ------------------------------------------------------------------------------------------------
>>>>>>>>
>>>>>>>> ------------------------------------------------------------------------------------------------
>>>>>>>> Forschungszentrum Jülich GmbH
>>>>>>>> 52425 Jülich
>>>>>>>> Sitz der Gesellschaft: Jülich
>>>>>>>> Eingetragen im Handelsregister des Amtsgerichts Düren Nr. HR B 3498
>>>>>>>> Vorsitzender des Aufsichtsrats: MinDir Stefan Müller
>>>>>>>> Geschäftsführung: Prof. Dr. Astrid Lambrecht (Vorsitzende),
>>>>>>>> Karsten Beneke (stellv. Vorsitzender), Prof. Dr. Ir. Pieter Jansens
>>>>>>>>
>>>>>>>> ------------------------------------------------------------------------------------------------
>>>>>>>>
>>>>>>>> ------------------------------------------------------------------------------------------------
>>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> ------------------------------------------------------------------------------------------------
>>>>>>>
>>>>>>> ------------------------------------------------------------------------------------------------
>>>>>>> Forschungszentrum Jülich GmbH
>>>>>>> 52425 Jülich
>>>>>>> Sitz der Gesellschaft: Jülich
>>>>>>> Eingetragen im Handelsregister des Amtsgerichts Düren Nr. HR B 3498
>>>>>>> Vorsitzender des Aufsichtsrats: MinDir Stefan Müller
>>>>>>> Geschäftsführung: Prof. Dr. Astrid Lambrecht (Vorsitzende),
>>>>>>> Karsten Beneke (stellv. Vorsitzender), Prof. Dr. Ir. Pieter Jansens
>>>>>>>
>>>>>>> ------------------------------------------------------------------------------------------------
>>>>>>>
>>>>>>> ------------------------------------------------------------------------------------------------
>>>>>>>
>>>>>>
>>>>>
>>>>> --
>>>>> Best Regards
>>>>> Elvis
>>>>>
>>>>
>>>>
>>>>
>>>> ------------------------------------------------------------------------------------------------
>>>>
>>>> ------------------------------------------------------------------------------------------------
>>>> Forschungszentrum Jülich GmbH
>>>> 52425 Jülich
>>>> Sitz der Gesellschaft: Jülich
>>>> Eingetragen im Handelsregister des Amtsgerichts Düren Nr. HR B 3498
>>>> Vorsitzender des Aufsichtsrats: MinDir Stefan Müller
>>>> Geschäftsführung: Prof. Dr. Astrid Lambrecht (Vorsitzende),
>>>> Karsten Beneke (stellv. Vorsitzender), Prof. Dr. Ir. Pieter Jansens
>>>>
>>>> ------------------------------------------------------------------------------------------------
>>>>
>>>> ------------------------------------------------------------------------------------------------
>>>>
>>>
>>>
>>>
>>> ------------------------------------------------------------------------------------------------
>>>
>>> ------------------------------------------------------------------------------------------------
>>> Forschungszentrum Jülich GmbH
>>> 52425 Jülich
>>> Sitz der Gesellschaft: Jülich
>>> Eingetragen im Handelsregister des Amtsgerichts Düren Nr. HR B 3498
>>> Vorsitzender des Aufsichtsrats: MinDir Stefan Müller
>>> Geschäftsführung: Prof. Dr. Astrid Lambrecht (Vorsitzende),
>>> Karsten Beneke (stellv. Vorsitzender), Prof. Dr. Ir. Pieter Jansens
>>>
>>> ------------------------------------------------------------------------------------------------
>>>
>>> ------------------------------------------------------------------------------------------------
>>>
>>
>>
>>
>> ------------------------------------------------------------------------------------------------
>>
>> ------------------------------------------------------------------------------------------------
>> Forschungszentrum Jülich GmbH
>> 52425 Jülich
>> Sitz der Gesellschaft: Jülich
>> Eingetragen im Handelsregister des Amtsgerichts Düren Nr. HR B 3498
>> Vorsitzender des Aufsichtsrats: MinDir Stefan Müller
>> Geschäftsführung: Prof. Dr. Astrid Lambrecht (Vorsitzende),
>> Karsten Beneke (stellv. Vorsitzender), Prof. Dr. Ir. Pieter Jansens
>>
>> ------------------------------------------------------------------------------------------------
>>
>> ------------------------------------------------------------------------------------------------
>>
>
>
>
> ------------------------------------------------------------------------------------------------
>
> ------------------------------------------------------------------------------------------------
> Forschungszentrum Jülich GmbH
> 52425 Jülich
> Sitz der Gesellschaft: Jülich
> Eingetragen im Handelsregister des Amtsgerichts Düren Nr. HR B 3498
> Vorsitzender des Aufsichtsrats: MinDir Stefan Müller
> Geschäftsführung: Prof. Dr. Astrid Lambrecht (Vorsitzende),
> Karsten Beneke (stellv. Vorsitzender), Prof. Dr. Ir. Pieter Jansens
>
> ------------------------------------------------------------------------------------------------
>
> ------------------------------------------------------------------------------------------------
>
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Received on Fri Oct 25 2024 - 07:00:02 PDT
