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-us...@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-us...@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-us...@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-us...@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
