Okay, thank you very much!
Keep in touch 😃
Enrico
Il giorno mer 3 apr 2024 alle ore 11:09 Stephan Schott <
s.schott-verdugo.fz-juelich.de> ha scritto:
> Hi Enrico,
>
> As mentioned before, this should be fixed in Amber24, which should be
> released within a month, give or take. Let me know if it is not the 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 mié, 3 abr 2024 a la(s) 10:47 a.m., Enrico Martinez (
> jmsstarlight.gmail.com) escribió:
>
>> Thank you again Stephan for this information !!
>>
>> So I've tested the packmol utility with 10 different membrane proteins
>> and there is always a problem with the tleap parametrization in the case of
>> multimeric proteins due to the TER removed during the structure insertion.
>> Here is a typical output from the tleap for the case of 3 chain complexes.
>>
>> There is a bond of 123.829 angstroms between C and N atoms:
>> ------- .R<LYS 1542>.A<C 21> and .R<LEU 1543>.A<N 1>
>> FATAL: Atom .R<LYS 257>.A<OXT 23> does not have a type.
>> FATAL: Atom .R<LEU 258>.A<H1 20> does not have a type.
>> FATAL: Atom .R<LEU 258>.A<H2 21> does not have a type.
>> FATAL: Atom .R<LEU 258>.A<H3 22> does not have a type.
>> FATAL: Atom .R<LYS 514>.A<OXT 23> does not have a type.
>> FATAL: Atom .R<LEU 515>.A<H1 20> does not have a type.
>> FATAL: Atom .R<LEU 515>.A<H2 21> does not have a type.
>> FATAL: Atom .R<LEU 515>.A<H3 22> does not have a type.
>> FATAL: Atom .R<LYS 771>.A<OXT 23> does not have a type.
>> FATAL: Atom .R<LEU 772>.A<H1 20> does not have a type.
>> FATAL: Atom .R<LEU 772>.A<H2 21> does not have a type.
>> FATAL: Atom .R<LEU 772>.A<H3 22> does not have a type.
>>
>> When I fix it manually adding the TER records after OXT atom and rerun
>> TLEAP on the fixed pdb everything works fine.
>>
>> Would it be possible anyway to fix the issue in the future releases of
>> amber-tools in order that the processing of multi-subnets systems could be
>> more smooth ? ;-)
>>
>> Many thanks in advance !!
>>
>> Enrico
>>
>> Il giorno sab 30 mar 2024 alle ore 13:38 Stephan Schott <
>> s.schott-verdugo.fz-juelich.de> ha scritto:
>>
>>> Hi Enrico,
>>>
>>> For the packing process, the TER flags or chain IDs are not needed. They
>>> are only required for leap to signal it should not try to bind in between
>>> different chain IDs/TER flags. If you pack a system with missing TER flags,
>>> you can always add them to the packed system and reprocess it with leap.
>>>
>>> Again, just for you to be sure, check the missing loops are in "okeish"
>>> positions. You might want to add caps to avoid adding charges where you
>>> might not want to have them?
>>>
>>> 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, 29 mar 2024 a la(s) 12:13 p.m., Enrico Martinez (
>>> jmsstarlight.gmail.com) escribió:
>>>
>>>> Thanks a lot for these precautions, Stephan !
>>>>
>>>> Just to be clear in order that I understand if I do the things
>>>> correctly. So to remove the gap I just modelled the missed loop. Then I use
>>>> the pdb4amber to fix missed residues and add hydrogens using reduce:
>>>> pdb4amber -i ./test.pdb -o ./with_h.pdb -y -p --reduce --no-conect
>>>> --add-missing-atoms
>>>>
>>>> From this step, It looks OK but the chain IDs are missing ... Is it
>>>> critical for the preparation of the membrane system of the complex (which
>>>> is separated by the chain IDS A,B,C in initial pdb) using packmol ?
>>>>
>>>> Many thanks in advance !
>>>>
>>>> Enrico
>>>>
>>>> Il giorno mar 26 mar 2024 alle ore 10:13 Stephan Schott <
>>>> s.schott-verdugo.fz-juelich.de> ha scritto:
>>>>
>>>>> Hi,
>>>>>
>>>>> So, again, it is not packmol removing the TERs, but memembed. I think
>>>>> I figured out how to keep them in their code, and this might come to
>>>>> Amber24.
>>>>>
>>>>> Yes, this would be not ideal if not intended. Still, you should not
>>>>> trust blindly the outputs and double check the result of any tool you are
>>>>> using, to make sure the structure is indeed what you wanted. pdb4amber,
>>>>> leap, packmol-memgen, etc., are helper tools, but relevant aspects like
>>>>> protonation states or the structures being parsed could change along the
>>>>> way.
>>>>>
>>>>> 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 mar, 26 mar 2024 a la(s) 8:51 a.m., Enrico Martinez (
>>>>> jmsstarlight.gmail.com) escribió:
>>>>>
>>>>>> Thank you very much Stephan !
>>>>>>
>>>>>> So basically I could be an elegant solution just to fix the packmol
>>>>>> in order that it could keep TER for the next tleap processing ...
>>>>>>
>>>>>> BTW: if I use a dimer protein for packmol (where there is a TER
>>>>>> separator between each monomer) does it mean that the packmol will remove
>>>>>> the TER and on the next step the TLEAP will create the bond between two
>>>>>> monomers embedded into the membrane ? Sound not a great idea at all .. ;-D
>>>>>>
>>>>>> All the best,
>>>>>>
>>>>>> Enrico
>>>>>>
>>>>>> Il giorno lun 25 mar 2024 alle ore 20:04 Stephan Schott <
>>>>>> s.schott-verdugo.fz-juelich.de> ha scritto:
>>>>>>
>>>>>>> Hi,
>>>>>>>
>>>>>>> The problem doesn't have to do with how the protein is embedded,
>>>>>>> memembed or ppm/opm both do a nice job in most cases, is just that memembed
>>>>>>> deletes TERs. The --ppm flag will use opm locally, but the option is only
>>>>>>> available as a test in versions >23.5. Should be more stable in Amber 24.If
>>>>>>> you have a file oriented in the ppm/opm webserver, you should use the
>>>>>>> --preoriented flag.
>>>>>>>
>>>>>>> The N and C-terminal residues are formally different. The H1,H2 and
>>>>>>> H3 correspond to N-ter residues, but leap "thinks" those are normal
>>>>>>> residues, meaning that in the last case, you probably are missing a TER
>>>>>>> *before* those residues (the message of the 10 A bond should be a
>>>>>>> hint). Note that the file you should be editing if doing this
>>>>>>> """automatically""" with packmol-memgen is the packed file, not the input
>>>>>>> file (so probably bilayer_XXX.pdb).
>>>>>>>
>>>>>>> As long as you are aware of what is in your output file, and you are
>>>>>>> ok with the gaps, then you can go ahead. You could also consider doing some
>>>>>>> overlapping with structures from the AlphaFold DB, if you want to play
>>>>>>> around with that.
>>>>>>>
>>>>>>> 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 lun, 25 mar 2024 a la(s) 5:37 p.m., Enrico Martinez (
>>>>>>> jmsstarlight.gmail.com) escribió:
>>>>>>>
>>>>>>>> So.. for the test I took another structure for the same complex but
>>>>>>>> again have the same issue with the parametrization in the final step
>>>>>>>> (although the protein was embedded correctly):
>>>>>>>> /opt/site/ubuntu_22.04/amber/22b/bin/teLeap: Warning!
>>>>>>>> There is a bond of 10.448 angstroms between C and N atoms:
>>>>>>>> ------- .R<ASP 794>.A<C 11> and .R<ARG 795>.A<N 1>
>>>>>>>> FATAL: Atom .R<SER 372>.A<H1 12> does not have a type.
>>>>>>>> FATAL: Atom .R<SER 372>.A<H2 13> does not have a type.
>>>>>>>> FATAL: Atom .R<SER 372>.A<H3 14> does not have a type.
>>>>>>>> FATAL: Atom .R<ASN 420>.A<H1 15> does not have a type.
>>>>>>>> FATAL: Atom .R<ASN 420>.A<H2 16> does not have a type.
>>>>>>>> FATAL: Atom .R<ASN 420>.A<H3 17> does not have a type.
>>>>>>>> FATAL: Atom .R<LYS 462>.A<H1 23> does not have a type.
>>>>>>>> FATAL: Atom .R<LYS 462>.A<H2 24> does not have a type.
>>>>>>>> FATAL: Atom .R<LYS 462>.A<H3 25> does not have a type.
>>>>>>>> FATAL: Atom .R<ASP 477>.A<H1 13> does not have a type.
>>>>>>>> FATAL: Atom .R<ASP 477>.A<H2 14> does not have a type.
>>>>>>>> FATAL: Atom .R<ASP 477>.A<H3 15> does not have a type.
>>>>>>>> FATAL: Atom .R<VAL 511>.A<H1 17> does not have a type.
>>>>>>>> FATAL: Atom .R<VAL 511>.A<H2 18> does not have a type.
>>>>>>>> FATAL: Atom .R<VAL 511>.A<H3 19> does not have a type.
>>>>>>>> FATAL: Atom .R<ARG 795>.A<H1 25> does not have a type.
>>>>>>>> FATAL: Atom .R<ARG 795>.A<H2 26> does not have a type.
>>>>>>>> FATAL: Atom .R<ARG 795>.A<H3 27> does not have a type.
>>>>>>>>
>>>>>>>> /opt/site/ubuntu_22.04/amber/22b/bin/teLeap: Fatal Error!
>>>>>>>> Failed to generate parameters
>>>>>>>>
>>>>>>>> Exiting LEaP: Errors = 1; Warnings = 893; Notes = 1.
>>>>>>>>
>>>>>>>> will it be reasonable just to remove these H1,H2,H3 from indicated
>>>>>>>> amino acids ??
>>>>>>>>
>>>>>>>> I enclose the structure :-)
>>>>>>>>
>>>>>>>> Thank you !!
>>>>>>>>
>>>>>>>> Enrico
>>>>>>>>
>>>>>>>>
>>>>>>>> Il giorno lun 25 mar 2024 alle ore 15:37 Enrico Martinez <
>>>>>>>> jmsstarlight.gmail.com> ha scritto:
>>>>>>>>
>>>>>>>>> Well, firstly thank you very much for this information !
>>>>>>>>>
>>>>>>>>> Actually I thought about the missed TER in the processed pdb ...
>>>>>>>>> Should the -ppm work only for the pdb that has been produced by
>>>>>>>>> opm web served (with the added dummy atoms for the membrane plane)?
>>>>>>>>>
>>>>>>>>> Actually in my case I tried it without this option and the protein
>>>>>>>>> was perfectly embedded in the bilayer ! And yes I could solve the issue
>>>>>>>>> with the manual editing of the structure after it's embedding into the
>>>>>>>>> membrane. Finally, here is the original pdb (directly taken from the PDB)
>>>>>>>>> with the chains IDs and original TER records, which however also did not
>>>>>>>>> parametrize without my manual edition (tleap sent errors due to the
>>>>>>>>> hydrogen atoms that are present in this pdb .. )!!
>>>>>>>>>
>>>>>>>>> Many thanks in advance !!
>>>>>>>>>
>>>>>>>>> Enrico
>>>>>>>>>
>>>>>>>>> Il giorno lun 25 mar 2024 alle ore 14:32 Stephan Schott <
>>>>>>>>> s.schott-verdugo.fz-juelich.de> ha scritto:
>>>>>>>>>
>>>>>>>>>> Hi Enrico,
>>>>>>>>>>
>>>>>>>>>> You didn't tell us what line you are using with packmol-memgen,
>>>>>>>>>> but I assume you are aligning it to a membrane slab with the current
>>>>>>>>>> default, which is memembed. What I suspect happened there is a bad combi of
>>>>>>>>>> successive programs deleting information of the system: pdb4amber when
>>>>>>>>>> requested to fill missing atoms, deletes the chain ids, while memembed
>>>>>>>>>> seems to delete TER flags. With that, leap at the end is not aware of the
>>>>>>>>>> separated chains of the protein. You can either add the chain ids back
>>>>>>>>>> before running packmol-memgen, use ppm instead of memembed (added as test
>>>>>>>>>> with --ppm in Amber 23.5 or above), or do the manual fix you did by the end
>>>>>>>>>> before parametrizing (if using packmol-memgen for getting a suggestion for
>>>>>>>>>> the leap input, you can run it first without --parametrize, fix your packed
>>>>>>>>>> pdb file, and then add it).
>>>>>>>>>>
>>>>>>>>>> I will see if I can fix memembed so it doesn't delete TERs to
>>>>>>>>>> avoid this.
>>>>>>>>>>
>>>>>>>>>> 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, 22 mar 2024 a la(s) 4:59 p.m., Carlos Simmerling via
>>>>>>>>>> AMBER (amber.ambermd.org) escribió:
>>>>>>>>>>
>>>>>>>>>>> Enrico,
>>>>>>>>>>> in the file that you attached, there is a TER between ASN340 and
>>>>>>>>>>> GLU15
>>>>>>>>>>> (later in the new pdb file these are 338 and 339). because of
>>>>>>>>>>> that,
>>>>>>>>>>> pdb4amber will add the missing OXT to 338, and H1/H2/H3 to 339.
>>>>>>>>>>> that should
>>>>>>>>>>> be fine going into tleap as long as the TER stays there. But
>>>>>>>>>>> tleap doesn't
>>>>>>>>>>> recognize those as terminal residues, so somehow that TER must
>>>>>>>>>>> have been
>>>>>>>>>>> lost along the way before you ran tleap.
>>>>>>>>>>>
>>>>>>>>>>> but then I get confused, because the pdb file output by
>>>>>>>>>>> pdb4amber doesn't
>>>>>>>>>>> have H1/H2/H3 on SER372 (at least when I ran pdb4amber using
>>>>>>>>>>> your command
>>>>>>>>>>> on the pdb file that you attached). So again there seems to be
>>>>>>>>>>> things
>>>>>>>>>>> changed in the PDB that you end up giving to tleap.
>>>>>>>>>>>
>>>>>>>>>>> I would suggest focusing on how you go from the pdb output by
>>>>>>>>>>> pdb4amber
>>>>>>>>>>> into the one that you load into tleap.
>>>>>>>>>>> you might also consider trying the prepareforleap function in
>>>>>>>>>>> cpptraj.
>>>>>>>>>>> building just the protein in gas phase as a simple test might
>>>>>>>>>>> also be
>>>>>>>>>>> helpful, then you'll know if the pdb file at each step is set up
>>>>>>>>>>> properly.
>>>>>>>>>>> then you can do your membrane later.
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>> On Fri, Mar 22, 2024 at 11:32 AM Enrico Martinez via AMBER <
>>>>>>>>>>> amber.ambermd.org> wrote:
>>>>>>>>>>>
>>>>>>>>>>> > Dear Amber users !
>>>>>>>>>>> >
>>>>>>>>>>> > I am working on the preparation of the model for the GPCR
>>>>>>>>>>> protein using
>>>>>>>>>>> > pack-mol memgen utility of amber tools for creation of the
>>>>>>>>>>> membrane and the
>>>>>>>>>>> > parametrization of the complex.
>>>>>>>>>>> >
>>>>>>>>>>> > The initial structure was taken from the pdb, which has some
>>>>>>>>>>> missed loops.
>>>>>>>>>>> > Since I decided not to restore these missed fragments I
>>>>>>>>>>> removed all
>>>>>>>>>>> > hydrogens and then pre-processed the model using
>>>>>>>>>>> >
>>>>>>>>>>> > pdb4amber -i ./input.pdb -o ./output_ambpro.pdb -y -p
>>>>>>>>>>> --add-missing-atoms
>>>>>>>>>>> >
>>>>>>>>>>> > These re-added missed hydrogens and some of the missed heavy
>>>>>>>>>>> atoms.
>>>>>>>>>>> >
>>>>>>>>>>> > Then, on the final step of the creation of the membrane
>>>>>>>>>>> complex I got the
>>>>>>>>>>> > error during the tleap parametrization of the embedded model:
>>>>>>>>>>> >
>>>>>>>>>>> > There is a bond of 9.221 angstroms between C and N atoms:
>>>>>>>>>>> > ------- .R<ASP 798>.A<C 11> and .R<ARG 799>.A<N 1>
>>>>>>>>>>> > FATAL: Atom .R<ASN 338>.A<OXT 15> does not have a type.
>>>>>>>>>>> > FATAL: Atom .R<GLU 339>.A<H1 16> does not have a type.
>>>>>>>>>>> > FATAL: Atom .R<GLU 339>.A<H2 17> does not have a type.
>>>>>>>>>>> > FATAL: Atom .R<GLU 339>.A<H3 18> does not have a type.
>>>>>>>>>>> > FATAL: Atom .R<SER 372>.A<H1 12> does not have a type.
>>>>>>>>>>> > FATAL: Atom .R<SER 372>.A<H2 13> does not have a type.
>>>>>>>>>>> > FATAL: Atom .R<SER 372>.A<H3 14> does not have a type.
>>>>>>>>>>> > FATAL: Atom .R<ASN 420>.A<H1 15> does not have a type.
>>>>>>>>>>> > FATAL: Atom .R<ASN 420>.A<H2 16> does not have a type.
>>>>>>>>>>> > FATAL: Atom .R<ASN 420>.A<H3 17> does not have a type.
>>>>>>>>>>> > FATAL: Atom .R<LYS 462>.A<H1 23> does not have a type.
>>>>>>>>>>> > FATAL: Atom .R<LYS 462>.A<H2 24> does not have a type.
>>>>>>>>>>> > FATAL: Atom .R<LYS 462>.A<H3 25> does not have a type.
>>>>>>>>>>> > FATAL: Atom .R<ASP 477>.A<H1 13> does not have a type.
>>>>>>>>>>> > FATAL: Atom .R<ASP 477>.A<H2 14> does not have a type.
>>>>>>>>>>> > FATAL: Atom .R<ASP 477>.A<H3 15> does not have a type.
>>>>>>>>>>> > FATAL: Atom .R<VAL 511>.A<H1 17> does not have a type.
>>>>>>>>>>> > FATAL: Atom .R<VAL 511>.A<H2 18> does not have a type.
>>>>>>>>>>> > FATAL: Atom .R<VAL 511>.A<H3 19> does not have a type.
>>>>>>>>>>> > FATAL: Atom .R<LEU 538>.A<OXT 20> does not have a type.
>>>>>>>>>>> > FATAL: Atom .R<SER 539>.A<H1 12> does not have a type.
>>>>>>>>>>> > FATAL: Atom .R<SER 539>.A<H2 13> does not have a type.
>>>>>>>>>>> > FATAL: Atom .R<SER 539>.A<H3 14> does not have a type.
>>>>>>>>>>> > FATAL: Atom .R<LYS 595>.A<OXT 23> does not have a type.
>>>>>>>>>>> > FATAL: Atom .R<TRP 596>.A<H1 25> does not have a type.
>>>>>>>>>>> > FATAL: Atom .R<TRP 596>.A<H2 26> does not have a type.
>>>>>>>>>>> > FATAL: Atom .R<TRP 596>.A<H3 27> does not have a type.
>>>>>>>>>>> > FATAL: Atom .R<ARG 799>.A<H1 25> does not have a type.
>>>>>>>>>>> > FATAL: Atom .R<ARG 799>.A<H2 26> does not have a type.
>>>>>>>>>>> > FATAL: Atom .R<ARG 799>.A<H3 27> does not have a type.
>>>>>>>>>>> >
>>>>>>>>>>> > /opt/site/ubuntu_22.04/amber/22b/bin/teLeap: Fatal Error!
>>>>>>>>>>> > Failed to generate parameters
>>>>>>>>>>> >
>>>>>>>>>>> > Exiting LEaP: Errors = 1; Warnings = 860; Notes = 1.
>>>>>>>>>>> >
>>>>>>>>>>> >
>>>>>>>>>>> > So I carefully examined the structure of the complex created
>>>>>>>>>>> by packmol and
>>>>>>>>>>> > found that the TER records (in the gaps corresponded to the
>>>>>>>>>>> missing
>>>>>>>>>>> > fragments) were removed so tleap did not recognize it
>>>>>>>>>>> correctly. For
>>>>>>>>>>> > simplicity I added TER records and in other cases (where there
>>>>>>>>>>> is no gap) I
>>>>>>>>>>> > just removed H1,H2,H3 atoms that were added in the wrong way.
>>>>>>>>>>> After this I
>>>>>>>>>>> > could parametrize the complex.
>>>>>>>>>>> >
>>>>>>>>>>> > What could be the best way to overcome such issue ? I enclose
>>>>>>>>>>> the initial
>>>>>>>>>>> > PDB without hydrogen atoms (before processing by amber-tools)
>>>>>>>>>>> as a
>>>>>>>>>>> > template.
>>>>>>>>>>> >
>>>>>>>>>>> > 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), 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), 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), 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), 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), 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), 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), 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), 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), 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), Dr. Ir. Pieter Jansens
>
> ------------------------------------------------------------------------------------------------
>
> ------------------------------------------------------------------------------------------------
>
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Received on Wed Apr 03 2024 - 07:00:02 PDT
