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
>
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>
>
> 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
>
> ------------------------------------------------------------------------------------------------
>
> ------------------------------------------------------------------------------------------------
>
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Received on Fri Oct 25 2024 - 06:30:02 PDT
