[gmx-users] (no subject)

[Navneet Kumar Singh]

Yeah! I have read that.

uses -maxwarn 1 to produce .tpr file using grompp command as mentioned in
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
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>
> Virginia Tech Department of Biochemistry
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-- 






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_______________________________________________________

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*NAVNEET KUMAR*
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