Dear Alex, But g-x2top doesn't work till we define all atom types in .n2t file.
Thanks On 26-Nov-2017 9:34 PM, "Alexandr Nasedkin" <nased...@chalmers.se> wrote: Hi, You will need to have both ffbonded.itp and ffnonbonded.itp . atomname2type.n2t is needed for g_x2top to make it work correctly. Good luck. -Alex On 26/11/2017 10:52, Rakesh Pant wrote: > Dear, Alex > Does it mean, we do not need to define all the atomtypes in the .nt2 file. > It is enough to define all types in bonded and non-bonded itp. > > Thanks, > Rakesh > > > > <https://mailtrack.io/> Sent with Mailtrack > <https://mailtrack.io/install?source=signature&lang=en&refer > ral=rakesh.p...@students.iiserpune.ac.in&idSignature=22> > > On Sun, Nov 26, 2017 at 3:27 PM, Alexandr Nasedkin <nased...@chalmers.se> > wrote: > > Edit the content of you ffnonbonded.itp file approximately this way: >> >> [ atomtypes ] >> ;name at.num mass charge ptype sigma epsilon >> C 14 12.00 1.08 A 0.44000 0.63 ; >> OCE 8 15.999400 -0.70 A 0.35400 0.159705 ; C-O-C >> Bridging Oxygen; >> OCH 8 15.999400 -0.51 A 0.35400 0.159705 ; C-O-H >> Oxygen; >> >> HCO 1 1.008000 0.32 A 0.04490 0.235725 ; H-O-C >> Hydrogen; >> .... >> >> You would need to search literature for respective ff parameters: all the >> above parameters are taken from another topology to give a template. >> >> >> -Alex >> >> >> On 26/11/2017 10:37, Rakesh Pant wrote: >> >> Dear Alex, >>> If I use O atoms to define the respective functional groups, then how >>> to >>> include the C atoms present in the molecule. >>> >>> Thanks, >>> Rakesh >>> >>> >>> >>> <https://mailtrack.io/> Sent with Mailtrack >>> <https://mailtrack.io/install?source=signature&lang=en&refer >>> ral=rakesh.p...@students.iiserpune.ac.in&idSignature=22> >>> >>> On Sun, Nov 26, 2017 at 3:08 PM, Alexandr Nasedkin <nased...@chalmers.se >>> > >>> wrote: >>> >>> Hi, >>> >>>> As I understood the problem, you need to distinguish between surface and >>>> buried carbons? >>>> >>>> You could define two atomtypes that differ in name and use it to process >>>> with x2top. >>>> >>>> Below is an example of *.n2t lines. You would need to change the charges >>>> and bondlengthes. >>>> >>>> ... >>>> >>>> O OCH -1.05 15.9994 2 C 0.154 H 0.1 ; oxygen, -OH >>>> group >>>> O OCE -1.05 15.9994 2 C 0.154 C 0.154 ; bridge >>>> oxygen >>>> >>>> ... >>>> >>>> Then you need *.n2t file in your ff. >>>> >>>> Good luck! >>>> >>>> >>>> -Alex >>>> >>>> >>>> On 25/11/2017 22:06, Justin Lemkul wrote: >>>> >>>> >>>> On 11/25/17 3:31 PM, Rakesh Pant wrote: >>>>> >>>>> But then I how will include the C atom (which is also one of the >>>>> >>>>>> atomtypes)? >>>>>> >>>>>> No idea, but I know people on this list have dealt with graphene oxide >>>>>> >>>>> before, so hopefully someone else chimes in. >>>>> >>>>> -Justin >>>>> >>>>> >>>>> -- >>>>> >>>> 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. >> >> > > -- 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.