Thank you very much Stephan !!
Actually I double checked everything and indeed the problem persists only
when I add cardiolipins to the systems so this could be the major issue in
the case of this complex system. Anyway thank you again and hope to see the
bug fix in the future ! ;-D
Your sincerely
Enrico
Il giorno ven 23 ago 2024 alle ore 13:32 Stephan Schott <
s.schott-verdugo.fz-juelich.de> ha scritto:
> Hi,
>
> Ok, what happens is a very misfortunate set of things going wrong at the
> same time.
>
> -You are requesting cardiolipins. For that I cleanup/standardize the pdb
> with pdb4amber, and make a temp pdb file with leap, to have the appropriate
> residue numbers to make the bonds of the cardiolipin in the parametrization
> step.
> -Your structure has cysteines that can form disulfide bridges (check
> this!), so pdb4amber adds connect flags to the intermediate file.
> -At the same time, you have more than 100000 atoms, so the atom number
> counter was reset at some point. The connect flags read by leap try to make
> bonds between water molecules instead of in the protein.
>
> A dirty workaround:
> -Open cli_clean.pdb and delete the connect flags at the end of the file
> (or with sed if scripted)
> -Run tleap -f leap_cli.in. Make sure a cli_temp.pdb is generated.
> -Rerun packmol-memgen with the exact same command line as you did before.
> It will fail, as cli_clean.pdb will be regenerated by pdb4amber.
> -Open cli_clean.pdb and delete the connect flags at the end of the file
> again.
> -Run tleap -f leap.in. That should generate the topology already. With
> that you will have to do the initial minimization steps yourself.
>
> I'll think on how to fix this case for the next release. And double check
> that disulfide bridge.
>
> 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, 23 ago 2024 a la(s) 11:18 a.m., Stephan Schott (
> s.schott-verdugo.fz-juelich.de) escribió:
>
>> Hi,
>>
>> Aside from telling you that you should have a look at the structure and
>> output file at the position of the error-causing waters, it would not be
>> possible to suggest you where the error lies without having the files to
>> try and reproduce the error on my end. Feel free to send them to me
>> internally if you'd like.
>>
>> 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, 23 ago 2024 a la(s) 11:01 a.m., Enrico Martinez via AMBER (
>> amber.ambermd.org) escribió:
>>
>>> Dear Amber users !
>>>
>>> I am using packmol-memgen for the preparation of GPCR system in water
>>> with
>>> following parameters
>>>
>>> /amber/22b/bin/packmol-memgen --pdb gpcr.pdb --lipids POPC:TOCL --salt_c
>>> Na+ --ffprot ff14SB --fflip lipid21 --ratio 90:10 --keepligs
>>> --ligand_param
>>> lig.frcmod:lig.lib --parametrize --minimize
>>>
>>> Briefly, it produces bilayer with the correctly inserted protein but at
>>> the final step of parametrization I got the following error:
>>>
>>> > SYS = loadpdb cli_clean.pdb
>>> Loading PDB file: ./cli_clean.pdb
>>> Matching PDB residue names to LEaP variables.
>>> Mapped residue CYX, term: Terminal/beginning, seq. number: 0 to: NCYX.
>>> Mapped residue LYS, term: Terminal/last, seq. number: 307 to: CLYS.
>>> Bond: maximum coordination exceeded on .R<WAT 19447>.A<H2 3>
>>> Bond: Maximum coordination exceeded on .R<WAT 19877>.A<H1 2>
>>> -- setting atoms pert=true overrides default limits
>>> ATOMS NOT BONDED: .R<WAT 19447>.A<H2 3> .R<WAT 19877>.A<H1 2>
>>>
>>> indicating that there is some problem with water in the prepared system
>>>
>>> How could this issue be solved ?
>>>
>>> Many thanks in advance
>>>
>>> Enrico
>>> _______________________________________________
>>> 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
>
> ------------------------------------------------------------------------------------------------
>
> ------------------------------------------------------------------------------------------------
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Aug 23 2024 - 05:00:02 PDT
