[gmx-users] (no subject)

[Navneet Kumar Singh]

Do I have to add vsite3 information from unk.itp to system.top files?

-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
>
> ==================================================
>
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> Gromacs Users mailing list
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