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 <jalem...@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
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Office: 301 Fralin Hall
Lab: 303 Engel Hall
Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061
jalem...@vt.edu | (540) 231-3129
http://www.thelemkullab.com
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