Sorry for the confusion, Tsjerk. Thanks. On Thu, Mar 4, 2010 at 11:47 AM, Tsjerk Wassenaar <tsje...@gmail.com> wrote:
> Hi Dian, > > Now why didn't I guess that you were trying on data obtained from > Amber?! Maybe because you didn't explicitly mentioned it. It always > helps to give a full account of what you were trying. > > Anyway, I don't know the format of the top of my head, so you'll have > to look in another pdb file and copy/edit the line (I think it's > angles and then lengths, all %8.3f, but I'm not sure), or you have to > check the pdb format at www.rcsb.org/pdb > > Hope it helps, > > Tsjerk > > On Thu, Mar 4, 2010 at 6:04 PM, Dian Jiao <oscarj...@gmail.com> wrote: > > Hi Tsjerk, > > > > My gromacs is 4.0.4. > > > > As it turns out, I do not have a CRYST1 keyword in my pdb file, so I > guess > > the box is not defined yet. The pdb was taken from the trajectory of > AMBER > > simulation, so it starts with the keyword "REMARK". How do I include box > > dimensions in pdb file then? Just add "CRYST1 24 24 24" in the first > line? > > By the way is it CRYST1 or CRYSTL? > > > > And the command I was running was "g_mindist -f 1001.pdb -n 1001.ndx -od > > 1001_C". > > > > Dian > > > > On Thu, Mar 4, 2010 at 12:38 AM, Tsjerk Wassenaar <tsje...@gmail.com> > wrote: > >> > >> Hi Dian, > >> > >> Which version of gromacs are you using? Can you assert that the pdb > >> file has the correct box? It should have a line starting with CRYST1 > >> (grep "^CRYST1" file.pdb). Some versions of gromacs (3.3.2 I think) > >> didn't write the CRYST1 record, and thus disallow PBC related > >> operations. > >> > >> Cheers, > >> > >> Tsjerk > >> > >> On Thu, Mar 4, 2010 at 8:08 AM, Dian Jiao <oscarj...@gmail.com> wrote: > >> > The box is 24X24X24 (Angstrom). The dummy atom I added at the end is > >> > about > >> > 31 A away from the closest water in the box. But if it is periodic, > >> > shouldn't there be waters near the dummy too? > >> > > >> > On Wed, Mar 3, 2010 at 10:29 PM, Mark Abraham < > mark.abra...@anu.edu.au> > >> > wrote: > >> >> > >> >> On 4/03/2010 11:30 AM, Dian Jiao wrote: > >> >>> > >> >>> Hi Gromacs users, > >> >>> > >> >>> I was trying to compute minimum distance between groups in a cubic > >> >>> water > >> >>> box with g_mindist using periodic boundary condition. In order to > test > >> >>> this, I added one more "atom" which is far away from any of the > other > >> >>> atoms in the pdb file. The mindist between that atom and all the > >> >>> waters > >> >>> were computed. The output of g_mindist is 3.089281e+00. (the unit is > >> >>> nm, > >> >>> right?) > >> >> > >> >> You haven't said how big your box is, or how far "far away" is, so we > >> >> can't tell whether you think 3nm is too big, too small, etc. > >> >> > >> >>> The manual shows that pbc is one of the option of g_mindist, but > isn't > >> >>> the default "yes"? I even tried with "-pbc" in the command, still > did > >> >>> not work. Can anyone tell me how to turn on PBC in g_mindist? > >> >> > >> >> See g_mindist -h. The -pbc flag turns PBC on, -nopbc turns it off. > >> >> > >> >> Mark > >> >> -- > >> >> gmx-users mailing list gmx-users@gromacs.org > >> >> http://lists.gromacs.org/mailman/listinfo/gmx-users > >> >> Please search the archive at http://www.gromacs.org/search before > >> >> posting! > >> >> Please don't post (un)subscribe requests to the list. Use the www > >> >> interface or send it to gmx-users-requ...@gromacs.org. > >> >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php > >> > > >> > > >> > -- > >> > gmx-users mailing list gmx-users@gromacs.org > >> > http://lists.gromacs.org/mailman/listinfo/gmx-users > >> > Please search the archive at http://www.gromacs.org/search before > >> > posting! > >> > Please don't post (un)subscribe requests to the list. Use the > >> > www interface or send it to gmx-users-requ...@gromacs.org. > >> > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > >> > > >> > >> > >> > >> -- > >> Tsjerk A. Wassenaar, Ph.D. > >> > >> Computational Chemist > >> Medicinal Chemist > >> Neuropharmacologist > >> -- > >> gmx-users mailing list gmx-users@gromacs.org > >> http://lists.gromacs.org/mailman/listinfo/gmx-users > >> Please search the archive at http://www.gromacs.org/search before > posting! > >> Please don't post (un)subscribe requests to the list. Use the > >> www interface or send it to gmx-users-requ...@gromacs.org. > >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > > > > > -- > > gmx-users mailing list gmx-users@gromacs.org > > http://lists.gromacs.org/mailman/listinfo/gmx-users > > Please search the archive at http://www.gromacs.org/search before > posting! > > Please don't post (un)subscribe requests to the list. Use the > > www interface or send it to gmx-users-requ...@gromacs.org. > > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > > > > > -- > Tsjerk A. Wassenaar, Ph.D. > > Computational Chemist > Medicinal Chemist > Neuropharmacologist > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php >
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