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
>
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> 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
>> >> _______________________________________________
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>> >> 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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> 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),
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Received on Fri May 17 2024 - 02:30:02 PDT
