[gmx-users] Getting ligand's topology

[Mahdi Sobati Nezhad]

can I use SWISSPARAM or MATCH servers?!

On Wed, 22 Aug 2018 23:50 Justin Lemkul, <jalemkul at vt.edu> wrote:

>
>
> On 8/22/18 3:18 PM, Mahdi Sobati Nezhad wrote:
> > Thanks, do acpype is for charmm?!
> >
> No, it is for AMBER.
>
> -Justin
>
> > 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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> >>>>>>>> --
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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
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> >>>
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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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