Right, thank you very much for your very useful suggestions Thomas !
With best wishes
Enrico
Il giorno mar 28 mar 2023 alle ore 13:19 Steinbrecher, Thomas <
thomas.steinbrecher.roche.com> ha scritto:
> Hi Enrico,
>
> I prefer to work from .mol2 files instead of .lib, but both formats should
> work fine as long as leap recognizes your residues. Loading one frcmod
> should be fine, that one is parsed by atom types, so both ligands will be
> covered, whatever they are named.
>
> Kind Regards,
>
> Thomas
>
> On Tue, Mar 28, 2023 at 12:02 PM Enrico Martinez <jmsstarlight.gmail.com>
> wrote:
>
>> P.S. just a quick update:
>> so I renamed 'lig' to 'lih' in the lib file and eventually tleap created
>> the correct topology with two different residues lig and lih.
>>
>> Should everything work fine from this point ?
>>
>> I would like to specify also that in the second tleap script I did not
>> use a .frcmod file for the second ligand since I have only lig.frcmod
>> produced by antechamber for the first ligand. :-)
>>
>> Il giorno mar 28 mar 2023 alle ore 11:52 Enrico Martinez <
>> jmsstarlight.gmail.com> ha scritto:
>>
>>> Thank you very much, Thomas !
>>> Actually, the lih.lib file (created for the second ligand via the first
>>> tleap script) contains the following string
>>> !!index array str
>>> "lih"
>>>
>>> ... but then
>>> !entry.lih.unit.name single str
>>> "lig"
>>>
>>> that indeed could rename it back since the created lih.parmtop contains
>>> %FORMAT
>>> lig
>>>
>>> indicating that in any topology this residue would be still considered
>>> as 'lig' :-)
>>>
>>>
>>> Just a minor question:
>>> do I need mandatory a lib file for my case (dealing with the replicas of
>>> the same residues that should have different name) or alternatively I may
>>> use some trick in the second tleap script related to the parametrization of
>>> the complex ?
>>>
>>> Many thanks in advance!
>>>
>>> Enrico
>>>
>>> Il giorno mar 28 mar 2023 alle ore 10:56 Steinbrecher, Thomas <
>>> thomas.steinbrecher.roche.com> ha scritto:
>>>
>>>> Hi Enrico,
>>>>
>>>> switching between .mol2 and .lib formats may be the issue, the later
>>>> keeps track of the residue name on its own, so the lih = ... assignment
>>>> wont work maybe. My quick solution would be, open lih.lib (it is text),
>>>> replace all instances of "lig" with "lih" and rerun your second script.
>>>>
>>>> Kind Regards,
>>>>
>>>> Thomas
>>>>
>>>>
>>>> On Mon, Mar 27, 2023 at 6:58 PM Enrico Martinez <jmsstarlight.gmail.com>
>>>> wrote:
>>>>
>>>>> 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
>>>>>>
>>>>>
>>>>
>>>> --
>>>> *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 Tue Mar 28 2023 - 07:00:03 PDT
