Re: [AMBER] [Sender Not Verified] Re: Antechamber preparation of the system docked to two identical ligands

From: Enrico Martinez via AMBER <amber.ambermd.org>
Date: Mon, 27 Mar 2023 18:58:33 +0200

Thank you very much, Thomas !

Actually, I've already searched for the answer but ... :-)

Here is my first tleap script made according to your suggestions that load
the first lig, copy it to the second (lih) and creates parm files for the
ligands to check whether everything was OK. The script works perfectly fine
but in the lih.prmtop I see that it's defined as "lig" (so the residue was
automatically renamed during the copy ) .

source leaprc.gaff
lig = loadmol2 lig.mol2
lih = copy lig
check lig
check lih
loadamberparams lig.frcmod
saveoff lig lig.lib
saveoff lih lih.lib
saveamberparm lig lig.prmtop
saveamberparm lih lih.prmtop
quit


Here is the second script, which parametrize the whole complex. It works OK
but in the protein.parmtop I see the 'lig' two times so the 'lih'
disappears :-)

source leaprc.protein.ff19SB
source leaprc.water.opc
source leaprc.gaff
loadamberparams lig.frcmod
loadoff lig.lib
loadoff lih.lib
prot = loadpdb complex_for_amber.pdb
addIons prot Cl- 0
addIons prot Na+ 0
setbox prot centers
solvateoct prot TIP3PBOX 20.0
savepdb prot complex_300K.pdb
saveamberparm prot protein.prmtop protein.prmcrd
quit

So the question: how to copy lig to lig (assuming that the both are the
same unit) but keep the initial names in the final parmtop for these two
residues as :lig and :lih ?

Many thanks for the help !

Enrico


Il giorno lun 27 mar 2023 alle ore 18:19 Steinbrecher, Thomas <
thomas.steinbrecher.roche.com> ha scritto:

> Hi Enrico,
>
> Im sorry but I think there is no way around you looking through the leap
> manual and checking how leap handles and recognizes residues and assigns
> parameters. I'm happy to have a look at your leap input file if you like,
> but this kind of troubleshooting is tricky to do remotely...
>
> Kind regards,
>
> Thomas
>
> On Mon, Mar 27, 2023 at 6:13 PM Enrico Martinez <jmsstarlight.gmail.com>
> wrote:
>
>> 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
>>>>
>>>
>
> --
> *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
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Mar 27 2023 - 10:00:02 PDT
Custom Search