just a quick remark to add:
in the case when I save lih.lib file on the first step (when I added lih =
copy lig) and then use it during the second tleap execution (to parametrize
whole complex), it creates the protein.parmtop that contains 2 residues lig
(so the lih is automatically renamed to lig). I believe that something
should be added in the second tleap execution .
Il giorno lun 27 mar 2023 alle ore 18:01 Enrico Martinez <
jmsstarlight.gmail.com> ha scritto:
> Thank you very much Thomas!
>
> Actually in this case I have a problem on the last step for the
> parametrization of the complex.
>
> Basically, according to the tutorial, I call tleap two times
> 1) when I consider only the ligand to create lib.lib, lig.pdb, lig.prmtop
> and lig.rst7. On this step I copy lig to lih as you indicated and
> everything works well.
>
> 2) Then I load the complex containing protein + the both ligands in order
> to create protein.parmtop. Here I need to load also parameters for ligand
> (lig.frcmod and lig.lib). Since there are no parameters for the second
> replica (lih), this produces error. Do I need to specify somehow on this
> step that the lih is equal to the lig ?
>
> Many thanks in advance
>
> Enrico
>
> Il giorno lun 27 mar 2023 alle ore 15:52 Steinbrecher, Thomas <
> thomas.steinbrecher.roche.com> ha scritto:
>
>> Hi Enrico,
>>
>> you need to specify that lig and lih are the same in your leap input
>> file, as suggested in the first mail I wrote :-) Depending on how you load
>> your parameters, you could for example have these lines here in your
>> leap.in:
>>
>> LIG = loadmol2 <file.mol2>
>> LIH = copy LIG
>>
>> then leap would recognize residues called LIG and LIH and apply the same
>> parameters to them.
>>
>> Kind Regards,
>>
>> Thomas
>>
>>
>> On Mon, Mar 27, 2023 at 3:28 PM Enrico Martinez <jmsstarlight.gmail.com>
>> wrote:
>>
>>> Hello Thomas,
>>>
>>> I hope you are doing well !
>>>
>>> I have a small question regarding the protocol of the parametrization of
>>> the system with two identical ligands. Here are three possibilities for the
>>> parametrization:
>>>
>>> (1) if I specify the two replicas of the same ligands in the initial
>>> pdb as "lig" and "lih" and subsequently grep each unit from the complex for
>>> the parametrization using antechamber (so totally I run it two times, which
>>> could not be correct according to your previous message) everything works
>>> fine. In the protein.prmtop I have two units for lig and lih and it looks
>>> OK.
>>>
>>> (2) if I try to name the both units as "lig" and parametrize only one of
>>> them and then apply new parameters on the both replicas (in the initial
>>> pdb) it works also OK. In the parmtop file I have two identical units: lig,
>>> lig. But as I talked before the presence of two identical units would
>>> complicate analysis.
>>>
>>> (3) Finally in the case when I still keep in the model two different
>>> names "lig" and "lih" but run parametrization only one time (e.g. using
>>> only "lig"), obviously parmtop for the complex could not be created and
>>> tleap sent an error message that all atoms of "lih" did not have parameters.
>>>
>>> How could I fix the (3) in order that I could have two different names
>>> for the same unit in the model ? Or alternatively should I rename one of
>>> the "lig" in the case of the (2) after its parametrization ?
>>>
>>> Many thanks in advance !
>>>
>>> Enrico
>>>
>>> Il giorno ven 24 mar 2023 alle ore 10:11 Steinbrecher, Thomas <
>>> thomas.steinbrecher.roche.com> ha scritto:
>>>
>>>> Hi Enrico,
>>>>
>>>> Im not sure parameterizing twice is a good idea, your parameters may be
>>>> slightly different due to input structure bias, so you have two subtly
>>>> different 'identical' ligands in your system. What's wrong with
>>>> parameterizing the molecule once and using those parameters for both
>>>> residues? You can specify them later with e.g. ":lig,lih" but I'd really
>>>> recommend the ambmask chapter 23.1.1 of the Amber manual for more details
>>>> and examples, masks can be tricky to write and you need to make sure they
>>>> match what you really want to be selected, especially if you are aiming for
>>>> some semi-automated analysis later.
>>>>
>>>> Are you sure you want both molecules as the "ligand" in MMPBSA? Then
>>>> you'd be neglecting entropy effects twice leading to scores that are hard
>>>> to interpret. I'm not saying this is wrong, depending on what you aim for,
>>>> but it sounds like you are planning some pretty non-standard MMPBSA
>>>> calculations here.
>>>>
>>>> Kind Regards,
>>>>
>>>> Thomas
>>>>
>>>> On Thu, Mar 23, 2023 at 5:35 PM Enrico Martinez <jmsstarlight.gmail.com>
>>>> wrote:
>>>>
>>>>> Okay, thank you very much Thomas!
>>>>>
>>>>> To introduce more flexibility in the analysis routine, I decided to
>>>>> use two different names for identical molecules and reparametrize each
>>>>> twisely via antechamber using identical parameters .. So imagine that if I
>>>>> have :lig and :lih what should be amber mask to use with anti-MMPBSA.py to
>>>>> check and select the both of them at once as a ligand ? :-)
>>>>>
>>>>> Many thanks in advance
>>>>>
>>>>> Enrico
>>>>>
>>>>> Il giorno gio 23 mar 2023 alle ore 15:53 Steinbrecher, Thomas <
>>>>> thomas.steinbrecher.roche.com> ha scritto:
>>>>>
>>>>>> Hi Enrico,
>>>>>>
>>>>>> identical molecules need only be parameterized once. So you would use
>>>>>> antechamber (and parmchk/parmfit ?) to create ligand.mol2 (or .lib) files
>>>>>> describing your compound. Normally, identical molecules would then have the
>>>>>> same residue name in your system, but that is not mandatory, just
>>>>>> convention. So in your case, when building your system from a pdb file, you
>>>>>> need to tell leap what parameters to use for each residue name, so if your
>>>>>> ligands are called LIG and LI2, then these two entries need to be defined
>>>>>> in your leap input file, for example by the two commands I posted above.
>>>>>>
>>>>>> Kind Regards,
>>>>>>
>>>>>> Thomas
>>>>>>
>>>>>>
>>>>>>
>>>>>> On Thu, Mar 23, 2023 at 3:27 PM Enrico Martinez via AMBER <
>>>>>> amber.ambermd.org> wrote:
>>>>>>
>>>>>>> Okay, thank you !
>>>>>>>
>>>>>>> Regarding the renaming, should it be in principle possible to
>>>>>>> parametrize
>>>>>>> the complex with two identical residues having different names in the
>>>>>>> initial complex e.g. lig1 and lig2 or for such case I need to
>>>>>>> parametrize
>>>>>>> each ligand separately using antechamber ?
>>>>>>>
>>>>>>> BTW, I've just executed mmgbsa using :lig mask and it seems it's
>>>>>>> summarized
>>>>>>> all the values resulting from from the calculations for both
>>>>>>> residues, so
>>>>>>> .. :- )
>>>>>>>
>>>>>>> Enrico
>>>>>>>
>>>>>>> Il giorno gio 23 mar 2023 alle ore 15:08 Carlos Simmerling <
>>>>>>> carlos.simmerling.gmail.com> ha scritto:
>>>>>>>
>>>>>>> > but if you want it for mmgbsa then this won't work... maybe
>>>>>>> renaming the
>>>>>>> > second ligand is better
>>>>>>> >
>>>>>>> > On Thu, Mar 23, 2023 at 10:06 AM Carlos Simmerling <
>>>>>>> > carlos.simmerling.gmail.com> wrote:
>>>>>>> >
>>>>>>> >> you can try making a for loop in cpptraj, you can loop over all
>>>>>>> >> occurrences of the ligand and write the analysis separately for
>>>>>>> each ligand
>>>>>>> >> instance, then only use the data file that you want. you could
>>>>>>> also modify
>>>>>>> >> the script to only analyze the first occurrence, but that would
>>>>>>> be a little
>>>>>>> >> more work in the script.
>>>>>>> >>
>>>>>>> >> try something like this, where you find matching residues, and
>>>>>>> then write
>>>>>>> >> the outputs using the residue number so you know later which is
>>>>>>> first.:
>>>>>>> >>
>>>>>>> >> parm prmtop.parm7
>>>>>>> >> trajin mdcrd.nc
>>>>>>> >> for residues A0 inmask :LIG
>>>>>>> >> rms \$A0 out rms.\$A0.dat nofit
>>>>>>> >> done
>>>>>>> >>
>>>>>>> >>
>>>>>>> >> On Thu, Mar 23, 2023 at 9:58 AM Enrico Martinez <
>>>>>>> jmsstarlight.gmail.com>
>>>>>>> >> wrote:
>>>>>>> >>
>>>>>>> >>> Thanks a lot, Carlos !
>>>>>>> >>>
>>>>>>> >>> Are there any other possibilities to select the ligand without
>>>>>>> residue
>>>>>>> >>> number ?
>>>>>>> >>>
>>>>>>> >>> E.g. I have two systems with two different proteins bound
>>>>>>> twisely to the
>>>>>>> >>> same ligand in chain A and chain B.
>>>>>>> >>> I need to use an atom mask, which would select the first
>>>>>>> occurrence of
>>>>>>> >>> the residue lig in the complex w/o specification of the residue
>>>>>>> number
>>>>>>> >>> which could differ in various systems..
>>>>>>> >>>
>>>>>>> >>> Many thanks in advance
>>>>>>> >>>
>>>>>>> >>> Enrico
>>>>>>> >>>
>>>>>>> >>> Il giorno gio 23 mar 2023 alle ore 13:19 Carlos Simmerling <
>>>>>>> >>> carlos.simmerling.gmail.com> ha scritto:
>>>>>>> >>>
>>>>>>> >>>> You can also use the residue number.
>>>>>>> >>>>
>>>>>>> >>>> On Thu, Mar 23, 2023, 8:17 AM Enrico Martinez via AMBER <
>>>>>>> >>>> amber.ambermd.org> wrote:
>>>>>>> >>>>
>>>>>>> >>>>> Dear Friends,
>>>>>>> >>>>>
>>>>>>> >>>>> Thank you very much for your kind suggestions!
>>>>>>> >>>>> Indeed this was an issue in my preparation setup using
>>>>>>> antechamber,
>>>>>>> >>>>> which
>>>>>>> >>>>> took both residues at the same time.
>>>>>>> >>>>>
>>>>>>> >>>>> BTW, I have a question related to the analysis of the system
>>>>>>> >>>>> containing two
>>>>>>> >>>>> identical ligands (the both named as LIG) bound in two
>>>>>>> different
>>>>>>> >>>>> monomers
>>>>>>> >>>>> of the complex. How could it be better to specify the atom mask
>>>>>>> >>>>> corresponding to a specific ligand (e.g. for mmgbsa) ? The
>>>>>>> only one
>>>>>>> >>>>> solution could be based only on the residue name in this case ?
>>>>>>> >>>>>
>>>>>>> >>>>> Many thanks in advance !
>>>>>>> >>>>>
>>>>>>> >>>>> Yours sincerely
>>>>>>> >>>>>
>>>>>>> >>>>> Enrico
>>>>>>> >>>>>
>>>>>>> >>>>> Il giorno mar 21 mar 2023 alle ore 17:27 Dr. Anselm Horn via
>>>>>>> AMBER <
>>>>>>> >>>>> amber.ambermd.org> ha scritto:
>>>>>>> >>>>>
>>>>>>> >>>>> > Dear Enrico,
>>>>>>> >>>>> >
>>>>>>> >>>>> > it is not clear to me what you are doing:
>>>>>>> >>>>> > If you already have the parameters for your ligand, then you
>>>>>>> need to
>>>>>>> >>>>> > load them only once into leap; the programs identifies the
>>>>>>> ligand
>>>>>>> >>>>> > according to its residue name, and thus it can deal with
>>>>>>> several
>>>>>>> >>>>> > identical residues in your (pdb) input, as long as the
>>>>>>> residue names
>>>>>>> >>>>> in
>>>>>>> >>>>> > your input and the parameter files do match.
>>>>>>> >>>>> >
>>>>>>> >>>>> > If you are still in the parameterization phase, then you
>>>>>>> also need
>>>>>>> >>>>> only
>>>>>>> >>>>> > one instance of your ligand.
>>>>>>> >>>>> >
>>>>>>> >>>>> > Best,
>>>>>>> >>>>> >
>>>>>>> >>>>> > Anselm
>>>>>>> >>>>> >
>>>>>>> >>>>> > Bioinformatik | NHR.FAU
>>>>>>> >>>>> > Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU)
>>>>>>> >>>>> > Germany
>>>>>>> >>>>> >
>>>>>>> >>>>> >
>>>>>>> >>>>> > Am 21.03.2023 um 17:00 schrieb Enrico Martinez via AMBER:
>>>>>>> >>>>> > > Dear Amber Users !
>>>>>>> >>>>> > >
>>>>>>> >>>>> > > I have an issue related to the preparation of the system
>>>>>>> >>>>> containing two
>>>>>>> >>>>> > > identical ligands present in two different binding sites.
>>>>>>> Actually
>>>>>>> >>>>> when I
>>>>>>> >>>>> > > try to copy the both units for the parametrization using
>>>>>>> >>>>> Antechamber it
>>>>>>> >>>>> > > says that it could not process two residues at the same
>>>>>>> time.
>>>>>>> >>>>> > >
>>>>>>> >>>>> > > Is there any preparation trick for such a case assuming
>>>>>>> that
>>>>>>> >>>>> everything
>>>>>>> >>>>> > > works fine with the same system containing only one ligand
>>>>>>> ?
>>>>>>> >>>>> > >
>>>>>>> >>>>> > > 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
>>>>>>> >>>>> >
>>>>>>> >>>>> _______________________________________________
>>>>>>> >>>>> 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
>>>>>>>
>>>>>>
>>>>>>
>>>>>> --
>>>>>> *Dr. Thomas Steinbrecher*
>>>>>> Principal Scientist CADD
>>>>>>
>>>>>> Roche Pharma Research and Early Development
>>>>>> Roche Innovation Center Basel
>>>>>> F. Hoffmann-La Roche Ltd
>>>>>> Bldg. 092/3.92
>>>>>> Grenzacherstrasse 124
>>>>>> 4070 Basel
>>>>>> Switzerland
>>>>>>
>>>>>> Phone +41 61 682 1319
>>>>>> mailto: thomas.steinbrecher.roche.com
>>>>>>
>>>>>
>>>>
>>>> --
>>>> *Dr. Thomas Steinbrecher*
>>>> Principal Scientist CADD
>>>>
>>>> Roche Pharma Research and Early Development
>>>> Roche Innovation Center Basel
>>>> F. Hoffmann-La Roche Ltd
>>>> Bldg. 092/3.92
>>>> Grenzacherstrasse 124
>>>> 4070 Basel
>>>> Switzerland
>>>>
>>>> Phone +41 61 682 1319
>>>> mailto: thomas.steinbrecher.roche.com
>>>>
>>>
>>
>> --
>> *Dr. Thomas Steinbrecher*
>> Principal Scientist CADD
>>
>> Roche Pharma Research and Early Development
>> Roche Innovation Center Basel
>> F. Hoffmann-La Roche Ltd
>> Bldg. 092/3.92
>> Grenzacherstrasse 124
>> 4070 Basel
>> Switzerland
>>
>> Phone +41 61 682 1319
>> mailto: thomas.steinbrecher.roche.com
>>
>
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Received on Mon Mar 27 2023 - 09:30:03 PDT
