[gmx-users] .coordinate(gro) file
Tasneem Kausar
tasneemkausar12 at gmail.com
Mon Nov 6 08:47:59 CET 2017
Fitsiou already suggested you to change the number of atoms at top second
line of the gro file.
On Mon, Nov 6, 2017 at 10:22 AM, rose rahmani <rose.rhmn93 at gmail.com> wrote:
> Hi dear
>
> yes,i did
>
> On Mon, Nov 6, 2017 at 12:07 AM, Fitsiou, Eleni <e.fitsiou at lancaster.ac.uk
> >
> wrote:
>
> > Hi, did you change the total number of atoms in your file ?
> > (the second line at the top of the gro file?)
> >
> > Best, Eleni
> > > On 5 Nov 2017, at 20:33, rose rahmani <rose.rhmn93 at gmail.com> wrote:
> > >
> > > Hi
> > >
> > > I have structure.gro file
> > >
> > > 32
> > > .
> > > .
> > > .
> > >
> > > 0ZnS S29 29 0.000 0.191 2.029
> > > 0ZnS S30 30 0.000 0.574 2.029
> > > 0ZnS Zn31 31 0.000 0.000 2.164
> > > 0ZnS Zn32 32 0.000 0.383 2.164
> > > 0.00000 0.00000 0.00000
> > >
> > > and AA.gro
> > >
> > > PRODRG COORDS
> > > 12
> > > 1PDB O 1 0.147 2.267 0.468
> > > 1PDB C 2 0.182 2.373 0.415
> > > 1PDB OC 3 0.151 2.486 0.453
> > > 1PDB CA 4 0.318 2.368 0.351
> > > 1PDB N 5 0.390 2.383 0.475
> > > 1PDB H2 6 0.368 2.471 0.516
> > > 1PDB H3 7 0.488 2.379 0.457
> > > 1PDB H1 8 0.364 2.309 0.538
> > > 1PDB CB 9 0.343 2.234 0.282
> > > 1PDB CG2 10 0.255 2.218 0.157
> > > 1PDB OG1 11 0.480 2.228 0.243
> > > 1PDB HG1 12 0.499 2.141 0.197
> > > 0.53100 0.53100 0.53100
> > > and i want to make one coordinate file for both of them(like
> > > protein-ligand tutorial)
> > >
> > > but when i copy structure.gro to the end of AA.gro to
> > make>>>complex.gro, i
> > > cant check it in any viewer like VMD,it seeems that complex.gro is not
> > > correctly modified,could you please tell me what is wrong?!
> > >
> > > Thank you
> > > --
> > > 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-request at 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-request at 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-request at gromacs.org.
>
More information about the gromacs.org_gmx-users
mailing list