Okay, I gotcha, so it might be a problem with cardiolipides since I created
two membranes i) one just DPPC and ii) another one adding a bit of
cardiolipins to test how it works. So the error is always in the case of
more complex membrane, I guess may be there is a cardiolipin, which is in
the interphase of protein (I am modeling a big 10 chain complex).
Thank you in advance
Enrico
Il giorno ven 17 mag 2024 alle ore 13:20 Stephan Schott <
s.schott-verdugo.fz-juelich.de> ha scritto:
> Hi,
>
> But is your system not packed, or what is the issue? The cli files are
> there to deal with cardiolipins. As there is no straight forward way to
> make branched molecules, I hack my way through it using leap and pdb4amber.
> That "error" is just because I didn't add a quit statement to the leap
> script, but should not affect the output. If the file is empty though, I
> would wonder what you are actually packing, what is in the input file, and
> so on. I cannot elaborate more without further info.
>
> Wrt to the second "issue" I also wouldn't know. Please try to share enough
> information so things are reproducible.
>
> Cheers,
>
> Stephan Schott Verdugo
> Biochemist
>
>
> Computational Biophysical Chemistry
> Institut für Bio- und Geowissenschaften / Bioinformatik (IBG-4)
> Forschungszentrum Jülich GmbH
> Wilhelm-Johnen-Straße, 52425 Jülich
> Germany
>
>
> ---------------------------------------------------------------------------------------------
>
> ---------------------------------------------------------------------------------------------
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> 52425 Jülich
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> El vie, 17 may 2024 a la(s) 11:10 a.m., Enrico Martinez (
> jmsstarlight.gmail.com) escribió:
>
>> Hello Stephan,
>> In the leap_cli.log file that was created automatically
>> I found only this *** Error: tl_getline(): not interactive, use stdio.
>>
>> btw on another system composed of DPPC lipids I found the leap.log
>> (wthout cli) with another error related to hydrogens of protein( this could
>> be an issue from my part !).
>> What is the difference between leap_cli.log and leap.log ??
>> Enrico
>>
>> Il giorno gio 16 mag 2024 alle ore 20:58 Stephan Schott <
>> s.schott-verdugo.fz-juelich.de> ha scritto:
>>
>>> Hi,
>>>
>>> You can pack the system without waters by making the packmol input file,
>>> and removing the lines associated with it (--notrun), but as Carlos
>>> mentions, it will probably not provide any speed benefit.
>>>
>>> I cannot help you with what you say without a clear error, coordinates,
>>> and/or log file.
>>>
>>> Cheers,
>>>
>>> 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 jue, 16 may 2024 a la(s) 5:19 p.m., Enrico Martinez via AMBER (
>>> amber.ambermd.org) escribió:
>>>
>>>> Ah okay thank you!
>>>> I have an additional question regarding the preparation of large systems
>>>> using Packmol Memgen. Actually trying to work with a really big
>>>> multi-subunit complex I could insert it into the membrane but on the
>>>> next
>>>> step I had a problem with tleap parametrization (activated directly in
>>>> the
>>>> packmol memgen), which was related to lipids (.. big distances between
>>>> some
>>>> of them). I also checked my structure (without the membrane) using tleap
>>>> and apparently there was no problem with it.
>>>> Thank you in advance!
>>>> Enrico
>>>>
>>>> Il giorno gio 16 mag 2024 alle ore 13:38 Carlos Simmerling <
>>>> carlos.simmerling.stonybrook.edu> ha scritto:
>>>>
>>>> > Since implicit solvent simulations don't employ PME, a cutoff is not
>>>> > usually used, leading to slow simulations of large systems. per-step
>>>> times
>>>> > are usually faster with explicit water, and the advantage comes from
>>>> faster
>>>> > sampling rates in implicit solvent. So I don't think this would be
>>>> helpful
>>>> > for you, at least not without additional optimizations of the implicit
>>>> > solvent code to speed up long-range interactions (for example, Alexey
>>>> > Onufriev has done work in that area).
>>>> >
>>>> >
>>>> > On Thu, May 16, 2024 at 5:02 AM Enrico Martinez via AMBER <
>>>> > amber.ambermd.org> wrote:
>>>> >
>>>> >> Dear Amber users !
>>>> >>
>>>> >> I am working on a membrane protein tutorial using packmol-memgen for
>>>> >> creation of a quite big system. Due to the size of the system I
>>>> wonder if
>>>> >> it would be possible to ignore the adding water in the system to
>>>> perform
>>>> >> simulation using implicit solvent. What options should be provided
>>>> for
>>>> >> packmol ?
>>>> >>
>>>> >> Many thanks in advance
>>>> >>
>>>> >> Enrico
>>>> >> _______________________________________________
>>>> >> AMBER mailing list
>>>> >> AMBER.ambermd.org
>>>> >> http://lists.ambermd.org/mailman/listinfo/amber
>>>> >>
>>>> >
>>>> >
>>>> > --
>>>> >
>>>> > ===================================================================
>>>> > Carlos Simmerling, Ph.D.
>>>> > Professor, Department of Chemistry
>>>> > Associate Director, Laufer Center for Physical and Quantitative
>>>> Biology
>>>> > Laufer Center, Room 119 Phone: 1-631-632-5424 Fax
>>>> 1-631-632-5405
>>>> > Stony Brook University E-mail:
>>>> > carlos.simmerling.stonybrook.edu <carlos.simmerling.gmail.com>
>>>> > Stony Brook, NY 11794-5115 Web: http://www.simmerlinglab.org
>>>> > ===================================================================
>>>> >
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>>> Vorsitzender des Aufsichtsrats: MinDir Stefan Müller
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>> Vorsitzender des Aufsichtsrats: MinDir Stefan Müller
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> Vorsitzender des Aufsichtsrats: MinDir Stefan Müller
> Geschäftsführung: Prof. Dr. Astrid Lambrecht (Vorsitzende),
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Received on Fri May 17 2024 - 06:00:02 PDT
