[gmx-users] Getting ligand's topology

Wed Aug 22 21:19:46 CEST 2018

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
>>>>>>>>>>> --
>>>>>>>>>>> Gromacs Users mailing list
>>>>>>>>>>>
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>>>>>>>>>>> --
>>>>>>>>>> *Regards,*
>>>>>>>>>> *Rahul *
>>>>>>>>>> --
>>>>>>>>>> Gromacs Users mailing list
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>>>>>>>>> --
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>>>>>>>> --
>>>>>>>> *Regards,*
>>>>>>>> *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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-- 
==================================================

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

==================================================