[gmx-users] (no subject)

Mon Aug 26 20:37:14 CEST 2019

I can't understand meaning of this "For all other GROMACS versions, you
will have to manually edit the topology to use "3fad" construction and
appropriate atom numbers." If I am using version other than the
Gromacs2016.x.

Can I get example of any topology file where these kind of construction've
for loan pair done manually in the topology file?

On Mon, Aug 26, 2019 at 11:57 PM Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 8/26/19 1:14 PM, Navneet Kumar Singh wrote:
> > Do I have to add vsite3 information from unk.itp to system.top files?
>
> That directive belongs in the topology to which it corresponds. If it is
> in unk.itp, then it is already in system.top. You don't need to include
> anything else.
>
> -Justin
>
> > -maxwarn 1 flag I checked in gromacs 16 version and it's running there.
> >
> > On Mon, 26 Aug 2019, 00:58 Justin Lemkul, <jalemkul at vt.edu> wrote:
> >
> >>
> >> On 8/25/19 2:17 PM, Navneet Kumar Singh wrote:
> >>> Yeah! I have read that.
> >>>
> >>> uses -maxwarn 1 to produce .tpr file using grompp command as mentioned
> in
> >> Since you are getting an error rather than a warning, that means you are
> >> not using GROMACS 2016.x, as the instructions I pointed to you say.
> >>
> >> If you want to use a different GROMACS version, you have to change the
> >> topology. Again see the link I provided for a description of what to do.
> >>
> >> -Justin
> >>
> >>> python script cgenff_charmm2gmx_py2.py
> >>>
> >>> output of cgenff_charmm2gmx_py2.py
> >>>
> >>
> _____________________________________________________________________________________________________________________________________________________________
> >>> NOTE 1: Code tested with python 2.7.12. Your version: 2.7.16 (default,
> >> Mar
> >>> 26 2019, 10:00:46)
> >>> [GCC 5.4.0 20160609]
> >>>
> >>> NOTE 2: Please be sure to use the same version of CGenFF in your
> >>> simulations that was used during parameter generation:
> >>> --Version of CGenFF detected in  unk.str : 4.0
> >>> --Version of CGenFF detected in  charmm36-jul2017.ff/forcefield.doc :
> 4.0
> >>>
> >>> NOTE 3: To avoid duplicated parameters, do NOT select the 'Include
> >>> parameters that are already in CGenFF' option when uploading a molecule
> >>> into CGenFF.
> >>>
> >>> NOTE 4: 1 lone pairs found in topology that are not in the mol2 file.
> >> This
> >>> is not a problem, just FYI!
> >>>
> >>> ============ DONE ============
> >>> Conversion complete.
> >>> The molecule topology has been written to unk.itp
> >>> Additional parameters needed by the molecule are written to unk.prm,
> >> which
> >>> needs to be included in the system .top
> >>>
> >>> PLEASE NOTE: lone pair construction requires duplicate host atom
> numbers,
> >>> which will make grompp complain
> >>> To produce .tpr files, the user MUST use -maxwarn 1 to circumvent this
> >> check
> >>
> ________________________________________________________________________________________________________________________________________________________________
> >>> After that I am using same -maxwarn 1 but still, it's giving error. It
> >> may
> >>> be some silly mistake please let me know.
> >>>
> >>>
> >>> On Sun, Aug 25, 2019 at 9:43 PM Justin Lemkul <jalemkul at vt.edu> wrote:
> >>>
> >>>> On 8/25/19 11:49 AM, Navneet Kumar Singh wrote:
> >>>>> Thank You Sir!
> >>>>>
> >>>>> Attached file can be downloaded from following link.
> >>>>>
> >>>>> https://fil.email/OR7Nsh0f
> >>>>> <https://fil.email/OR7Nsh0f?&showconfirmation=true>
> >>>>> ____________________________________________________________________
> >>>>> Error
> >>>>>
> >>>>> ERROR 1 [file unk.itp, line 497]:
> >>>>>      Duplicate atom index (23) in virtual_sites3
> >>>>> ___________________________________________________________________
> >>>>>
> >>>>> It support lone pair construction for halogens only. Please suggest
> >> some
> >>>>> alternatives.
> >>>> The link I provided before describes what you need to do. Please
> consult
> >>>> that information.
> >>>>
> >>>> -Justin
> >>>>
> >>>> --
> >>>> ==================================================
> >>>>
> >>>> Justin A. Lemkul, Ph.D.
> >>>> Assistant Professor
> >>>> Office: 301 Fralin Hall
> >>>> Lab: 303 Engel Hall
> >>>>
> >>>> Virginia Tech Department of Biochemistry
> >>>> 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
> >> Office: 301 Fralin Hall
> >> Lab: 303 Engel Hall
> >>
> >> Virginia Tech Department of Biochemistry
> >> 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
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> >> posting!
> >>
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> >> send a mail to gmx-users-request at gromacs.org.
> >>
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Office: 301 Fralin Hall
> Lab: 303 Engel Hall
>
> Virginia Tech Department of Biochemistry
> 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
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> posting!
>
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>
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_______________________________________________________

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