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
