[gmx-users] Getting ligand's topology
Bratin Kumar Das
177cy500.bratin at nitk.edu.in
Wed Aug 22 07:13:28 CEST 2018
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
>>>>>>>>> --
>>>>>>>>> Gromacs Users mailing list
>>>>>>>>>
>>>>>>>>> * Please search the archive at
>>>>>>>>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>>>>>>>>> posting!
>>>>>>>>>
>>>>>>>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>>>>>>>>
>>>>>>>>> * For (un)subscribe requests visit
>>>>>>>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users
>>>>>>>>>
>>>>>>>> or
>>>>>>
>>>>>>> send a mail to gmx-users-request at gromacs.org.
>>>>>>>>>
>>>>>>>>> --
>>>>>>>> *Regards,*
>>>>>>>> *Rahul *
>>>>>>>> --
>>>>>>>> Gromacs Users mailing list
>>>>>>>>
>>>>>>>> * Please search the archive at
>>>>>>>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>>>>>>>> posting!
>>>>>>>>
>>>>>>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>>>>>>>
>>>>>>>> * For (un)subscribe requests visit
>>>>>>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users
>>>>>>>>
>>>>>>> or
>>>>>
>>>>>> send a mail to gmx-users-request at gromacs.org.
>>>>>>>>
>>>>>>> --
>>>>>>> Gromacs Users mailing list
>>>>>>>
>>>>>>> * Please search the archive at
>>>>>>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>>>>>>> posting!
>>>>>>>
>>>>>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>>>>>>
>>>>>>> * For (un)subscribe requests visit
>>>>>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users
>>>>>>> or
>>>>>>> send a mail to gmx-users-request at gromacs.org.
>>>>>>>
>>>>>> --
>>>>>> *Regards,*
>>>>>> *Rahul *
>>>>>> --
>>>>>> Gromacs Users mailing list
>>>>>>
>>>>>> * Please search the archive at
>>>>>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>>>>>> posting!
>>>>>>
>>>>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>>>>>
>>>>>> * For (un)subscribe requests visit
>>>>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>>>>>> send a mail to gmx-users-request at gromacs.org.
>>>>>>
>>>>> --
>>>>> Gromacs Users mailing list
>>>>>
>>>>> * Please search the archive at
>>>>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>>>>> posting!
>>>>>
>>>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>>>>
>>>>> * For (un)subscribe requests visit
>>>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>>>>> send a mail to gmx-users-request at gromacs.org.
>>>>>
>>>> --
>>> ==================================================
>>>
>>> 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
>>>
>>> ==================================================
>>>
>>> --
>>> Gromacs Users mailing list
>>>
>>> * Please search the archive at
>>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>>> posting!
>>>
>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>>
>>> * For (un)subscribe requests visit
>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>>> send a mail to gmx-users-request at gromacs.org.
>>>
>>
> --
> ==================================================
>
> 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
>
> ==================================================
>
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/Support
> /Mailing_Lists/GMX-Users_List before posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>
More information about the gromacs.org_gmx-users
mailing list