[gmx-users] Getting ligand's topology
Mahdi Sobati Nezhad
mahdisobatinezhad at gmail.com
Wed Aug 22 21:18:25 CEST 2018
Thanks, do acpype is for charmm?!
On Wed, 22 Aug 2018 09:43 Bratin Kumar Das, <177cy500.bratin at nitk.edu.in>
wrote:
> Hi
> You can use acpype for generating the ligand topology. It's simple and
> easy
>
> On Mon, Aug 20, 2018 at 5:03 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
> >
> >
> > On 8/20/18 2:40 AM, Mahdi Sobati Nezhad wrote:
> >
> >> thanks for your taking time. and so on for a begginer like me there is
> no
> >> any way
> >>
> >
> > Well, there is if you're willing to invest the time in learning some
> > challenging concepts and some new software. But no one should expect that
> > for any given ligand, there is a perfect tool for magically giving you a
> > perfect topology. That's rarely the case.
> >
> > -Justin
> >
> >
> > On Mon, 20 Aug 2018 00:29 Justin Lemkul, <jalemkul at vt.edu> wrote:
> >>
> >>
> >>> On 8/19/18 10:20 AM, RAHUL SURESH wrote:
> >>>
> >>>> Hi.
> >>>>
> >>>> First, I feel grimaces users may not entertain other discussions in
> >>>>
> >>> grimace
> >>>
> >>>> forum. You can directly mail me if it’s something apart from gromacs.
> >>>>
> >>>> Then, I am not sure about other servers.
> >>>>
> >>>> Looking at your str file, I would say that it definitely need some
> work
> >>>>
> >>> on
> >>>
> >>>> our molecule. As I said before try zinc database.
> >>>>
> >>> I don't see how the ZINC database is relevant. Either the .mol2
> >>> submitted to the CGenFF server is valid or it is not.
> >>>
> >>> CGenFF is nice in that it tells you the potential problems with the
> >>> ligand topology. AFAIK, no other servers do. You get a "black box"
> >>> output that you're supposed to trust. The areas pinpointed by CGenFF
> >>> should be examined carefully. The parameters may actually be fine, but
> >>> the penalties are there to tell the user when there is a functional
> >>> group that is not well described by existing molecules in the CGenFF
> >>> database, from which the analogies are made.
> >>>
> >>> There is a CGenFF tutorial available online that walks a user through
> >>> the whole process. It requires subdividing a molecule into units that
> >>> can be parametrized easily; large molecules should always be broken
> down
> >>> into manageable pieces that have all the necessary degrees of freedom.
> >>>
> >>> The tutorial materials can be accessed here:
> >>> http://mackerell.umaryland.edu/~kenno/cgenff/download.php
> >>>
> >>> CHARMM/CGenFF parametrization assumes some familiarity with QM
> >>> calculations (geometry optimizations, potential energy scans,
> >>> interaction energies) but the methodology is published in great detail,
> >>> and the CGenFF paper itself is a worked example of how to parametrize a
> >>> molecule. While the developers have made every effort to make the
> >>> methodology publicly available, ligand parametrization and refinement
> is
> >>> still an advanced concept that is best suited for experienced users, as
> >>> knowledge of fundamental principles of MD, QM, and empirical energy
> >>> functions is required.
> >>>
> >>> -Justin
> >>>
> >>> Thank you
> >>>>
> >>>>
> >>>> On Sun, 19 Aug 2018 at 1:37 PM, Mahdi Sobati Nezhad <
> >>>> mahdisobatinezhad at gmail.com> wrote:
> >>>>
> >>>> thanks.
> >>>>> if I use MATCH server or swissparam, I can trust to their results?!
> >>>>>
> >>>>> And this is my error when I use CGenFF:
> >>>>> "readmol2 warning: non-unique atoms were renamed. Now processing
> >>>>>
> >>>> molecule
> >>>
> >>>> mae ..."
> >>>>>
> >>>>> And this is my output of penalty:
> >>>>>
> >>>>> * Toppar stream file generated by * CHARMM General Force Field
> (CGenFF)
> >>>>> program version 2.2.0 * For use with CGenFF version 4.0 * read rtf
> card
> >>>>> append * Topologies generated by * CHARMM General Force Field
> (CGenFF)
> >>>>> program version 2.2.0 * 36 1 ! "penalty" is the highest penalty score
> >>>>> of
> >>>>> the associated parameters. ! Penalties lower than 10 indicate the
> >>>>>
> >>>> analogy
> >>>
> >>>> is fair; penalties between 10 ! and 50 mean some basic validation is
> >>>>> recommended; penalties higher than ! 50 indicate poor analogy and
> >>>>>
> >>>> mandate
> >>>
> >>>> extensive validation/optimization. RESI mae 0.000 ! param penalty=
> >>>>>
> >>>> 198.400
> >>>
> >>>> ; charge penalty= 142.287 GROUP ! CHARGE CH_PENALTY ATOM C1 CG2R61
> >>>>>
> >>>> 0.227 !
> >>>
> >>>> 0.000 ATOM C2 CG2R61 -0.117 ! 2.688 ATOM C3 CG2R61 -0.003 ! 5.191 ATOM
> >>>>>
> >>>> C4
> >>>
> >>>> CG2R61 -0.117 ! 2.688 ATOM C5 CG2R61 0.227 ! 0.000 ATOM C6 CG2R61
> 0.217
> >>>>>
> >>>> !
> >>>
> >>>> 0.000 ATOM H1 HGR61 0.115 ! 0.000 ATOM H2 HGR61 0.115 ! 0.000 ATOM O1
> >>>>>
> >>>> OG301
> >>>
> >>>> -0.391 ! 0.000 ATOM O2 OG301 -0.391 ! 0.000 ATOM O3 OG301 -0.391 !
> 0.000
> >>>>> ATOM C7 CG331 -0.100 ! 0.000 ATOM H3 HGA3 0.090 ! 0.000 ATOM H4 HGA3
> >>>>>
> >>>> 0.090
> >>>
> >>>> ! 0.000 ATOM H5 HGA3 0.090 ! 0.000 ATOM C8 CG331 -0.100 ! 0.000 ATOM
> H6
> >>>>> HGA3 0.090 ! 0.000 ATOM H7 HGA3 0.090 ! 0.000 ATOM H8 HGA3 0.090 !
> >>>>> 0.000
> >>>>> ATOM C9 CG331 -0.100 ! 0.000 ATOM H9 HGA3 0.090 ! 0.000 ATOM H10 HGA3
> >>>>>
> >>>> 0.090
> >>>
> >>>> ! 0.000 ATOM H11 HGA3 0.090 ! 0.000 ATOM C10 CG3C51 0.317 ! 142.287
> >>>>>
> >>>> ATOM N1
> >>>
> >>>> NG3C51 -0.343 ! 101.066 ATOM C11 CG321 -0.072 ! 70.919 ATOM H12 HGA2
> >>>>>
> >>>> 0.090
> >>>
> >>>> ! 2.500 ATOM H13 HGA2 0.090 ! 2.500 ATOM C12 CG2R53 0.464 ! 90.248
> ATOM
> >>>>>
> >>>> N2
> >>>
> >>>> NG2R50 -0.515 ! 21.469 ATOM N3 NG3C51 -0.417 ! 87.522 ATOM H14 HGP1
> >>>>>
> >>>> 0.341 !
> >>>
> >>>> 3.424 ATOM C13 CG321 0.028 ! 26.713 ATOM H15 HGA2 0.090 ! 2.659 ATOM
> N4
> >>>>> NG3N1 -0.689 ! 58.305 ATOM C14 CG2R61 0.140 ! 19.097 ATOM C15 CG2R61
> >>>>>
> >>>> -0.110
> >>>
> >>>> ! 13.488 ATOM C16 CG2R61 0.036 ! 13.718 ATOM C17 CG2R61 -0.112 ! 0.000
> >>>>>
> >>>> ATOM
> >>>
> >>>> H16 HGR61 0.115 ! 0.000 ATOM C18 CG2R61 0.071 ! 0.000 ATOM C19 CG2R61
> >>>>> -0.089 ! 0.000 ATOM H17 HGR61 0.115 ! 0.000 ATOM S SG311 -0.210 !
> >>>>>
> >>>> 105.411
> >>>
> >>>> ATOM H18 HGP3 0.160 ! 4.359 ATOM H19 HGR62 0.144 ! 0.000 ATOM Cl1
> CLGR1
> >>>>> -0.152 ! 2.500 ATOM Cl2 CLGR1 -0.167 ! 0.000 ATOM HXT1 HGA1 0.090 !
> >>>>>
> >>>> 5.954
> >>>
> >>>> ATOM HXT2 HGA2 0.090 ! 2.659 ATOM HN HGP1 0.394 ! 9.368 ATOM LP1 LPH
> >>>>>
> >>>> 0.050
> >>>
> >>>> ! on Cl1 ATOM LP2 LPH 0.050 ! on Cl2
> >>>>>
> >>>>>
> >>>>> Thanks for your taking time
> >>>>>
> >>>>>
> >>>>> On Sat, 18 Aug 2018 22:31 RAHUL SURESH, <drrahulsuresh at gmail.com>
> >>>>>
> >>>> wrote:
> >>>
> >>>> I cannot assist you much with the description of your ligand. But what
> >>>>>>
> >>>>> I
> >>>
> >>>> have seen is, ring with N shows maximum penalities in most cases.
> >>>>>>
> >>>>>> When you optimise with mp2, the structure shows no much changes.
> >>>>>> So penalty is same most time.
> >>>>>>
> >>>>>> Try to download file from Zinc15 database which is most preferred
> file
> >>>>>> cgenff. Still the penalty may exist in cse of N in ring. It could
> >>>>>> be
> >>>>>> optimised using ffTK. Again I find your structure is pretty big
> which
> >>>>>>
> >>>>> will
> >>>>>
> >>>>>> be time consuming. Or you have to adapt divide and conquer method,
> >>>>>>
> >>>>> which
> >>>
> >>>> is
> >>>>>
> >>>>>> going to be complicated. So it’s your wise choice always. Maybe
> >>>>>> others,
> >>>>>> especially Dr. Justin or Dr. Mark could give you a better soln.
> >>>>>>
> >>>>>> Thank you
> >>>>>>
> >>>>>> On Sat, 18 Aug 2018 at 10:17 PM, Mahdi Sobati Nezhad <
> >>>>>> mahdisobatinezhad at gmail.com> wrote:
> >>>>>>
> >>>>>> Thanks for your help.
> >>>>>>> my ligand is three rings that connects with a carbon and this rings
> >>>>>>>
> >>>>>> have
> >>>>>
> >>>>>> Nitrogen, oxygen, sulfur, carbon and Chlor...
> >>>>>>> And high penaltys are just for that ring that contains Nitrogen,
> >>>>>>>
> >>>>>> carbon
> >>>
> >>>> and
> >>>>>>
> >>>>>>> sulfur
> >>>>>>> And so on my choice is just using ffTK?!
> >>>>>>>
> >>>>>>>
> >>>>>>> On Sat, 18 Aug 2018 21:05 RAHUL SURESH, <drrahulsuresh at gmail.com>
> >>>>>>>
> >>>>>> wrote:
> >>>>>
> >>>>>> Hi.
> >>>>>>>>
> >>>>>>>> To resolve the penalties are bit complicated. Tools like ffTK can
> >>>>>>>>
> >>>>>>> help
> >>>>>
> >>>>>> you
> >>>>>>>
> >>>>>>>> do it. But output from ffTK is as in charmm and henceforth it take
> >>>>>>>> additional work ( was difficult for me ) to modify it to Gromacs
> >>>>>>>>
> >>>>>>> acceptable
> >>>>>>>
> >>>>>>>> format.
> >>>>>>>>
> >>>>>>>> I personally don’t appreciate this method as it is very time
> >>>>>>>>
> >>>>>>> consuming
> >>>>>
> >>>>>> if
> >>>>>>
> >>>>>>> your structure is big and having penalties in dihedrals which again
> >>>>>>>>
> >>>>>>> make
> >>>>>>
> >>>>>>> it
> >>>>>>>
> >>>>>>>> complicated.
> >>>>>>>> Thank you
> >>>>>>>>
> >>>>>>>> On Sat, 18 Aug 2018 at 7:02 PM, Mahdi Sobati Nezhad <
> >>>>>>>> mahdisobatinezhad at gmail.com> wrote:
> >>>>>>>>
> >>>>>>>> Hi
> >>>>>>>>> I'm a begginer in taking ligand's topology from CGENFF and my
> >>>>>>>>>
> >>>>>>>> '.str'
> >>>>>
> >>>>>> file
> >>>>>>>
> >>>>>>>> have some high penalty numbers. What I can do?!
> >>>>>>>>> And how I can do validation and optimization?!
> >>>>>>>>> I read the FAQ in its server but I don't understand!!!
> >>>>>>>>> Thanks
> >>>>>>>>> --
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> >>>>>>>>>
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> >>>>>>>>> posting!
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> >>>>>>>>>
> >>>>>>>>> --
> >>>>>>>> *Regards,*
> >>>>>>>> *Rahul *
> >>>>>>>> --
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> >>>>>> *Rahul *
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> >>>>>
> >>>> --
> >>> ==================================================
> >>>
> >>> Justin A. Lemkul, Ph.D.
> >>> Assistant Professor
> >>> Virginia Tech Department of Biochemistry
> >>>
> >>> 303 Engel Hall
> >>> 340 West Campus Dr.
> >>> Blacksburg, VA 24061
> >>>
> >>> jalemkul at vt.edu | (540) 231-3129
> >>> http://www.thelemkullab.com
> >>>
> >>> ==================================================
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> >>
> > --
> > ==================================================
> >
> > Justin A. Lemkul, Ph.D.
> > Assistant Professor
> > Virginia Tech Department of Biochemistry
> >
> > 303 Engel Hall
> > 340 West Campus Dr.
> > Blacksburg, VA 24061
> >
> > jalemkul at vt.edu | (540) 231-3129
> > http://www.thelemkullab.com
> >
> > ==================================================
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