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, <jalem...@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 <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 > >> > >> -- > >> ================================================== > >> > >> 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 > >> > >> jalem...@vt.edu | (540) 231-3129 > >> http://www.thelemkullab.com > >> > >> ================================================== > >> > >> -- > >> Gromacs Users mailing list > >> > >> * Please search the archive at > >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > >> posting! > >> > >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > >> > >> * For (un)subscribe requests visit > >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > >> send a mail to gmx-users-requ...@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 > > jalem...@vt.edu | (540) 231-3129 > http://www.thelemkullab.com > > ================================================== > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.