Sorry for the confusion, Tsjerk. Thanks.<br><br><div class="gmail_quote">On Thu, Mar 4, 2010 at 11:47 AM, Tsjerk Wassenaar <span dir="ltr"><<a href="mailto:tsjerkw@gmail.com">tsjerkw@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Hi Dian,<br>
<br>
Now why didn't I guess that you were trying on data obtained from<br>
Amber?! Maybe because you didn't explicitly mentioned it. It always<br>
helps to give a full account of what you were trying.<br>
<br>
Anyway, I don't know the format of the top of my head, so you'll have<br>
to look in another pdb file and copy/edit the line (I think it's<br>
angles and then lengths, all %8.3f, but I'm not sure), or you have to<br>
check the pdb format at <a href="http://www.rcsb.org/pdb" target="_blank">www.rcsb.org/pdb</a><br>
<br>
Hope it helps,<br>
<font color="#888888"><br>
Tsjerk<br>
</font><div><div></div><div class="h5"><br>
On Thu, Mar 4, 2010 at 6:04 PM, Dian Jiao <<a href="mailto:oscarjiao@gmail.com">oscarjiao@gmail.com</a>> wrote:<br>
> Hi Tsjerk,<br>
><br>
> My gromacs is 4.0.4.<br>
><br>
> As it turns out, I do not have a CRYST1 keyword in my pdb file, so I guess<br>
> the box is not defined yet. The pdb was taken from the trajectory of AMBER<br>
> simulation, so it starts with the keyword "REMARK". How do I include box<br>
> dimensions in pdb file then? Just add "CRYST1 24 24 24" in the first line?<br>
> By the way is it CRYST1 or CRYSTL?<br>
><br>
> And the command I was running was "g_mindist -f 1001.pdb -n 1001.ndx -od<br>
> 1001_C".<br>
><br>
> Dian<br>
><br>
> On Thu, Mar 4, 2010 at 12:38 AM, Tsjerk Wassenaar <<a href="mailto:tsjerkw@gmail.com">tsjerkw@gmail.com</a>> wrote:<br>
>><br>
>> Hi Dian,<br>
>><br>
>> Which version of gromacs are you using? Can you assert that the pdb<br>
>> file has the correct box? It should have a line starting with CRYST1<br>
>> (grep "^CRYST1" file.pdb). Some versions of gromacs (3.3.2 I think)<br>
>> didn't write the CRYST1 record, and thus disallow PBC related<br>
>> operations.<br>
>><br>
>> Cheers,<br>
>><br>
>> Tsjerk<br>
>><br>
>> On Thu, Mar 4, 2010 at 8:08 AM, Dian Jiao <<a href="mailto:oscarjiao@gmail.com">oscarjiao@gmail.com</a>> wrote:<br>
>> > The box is 24X24X24 (Angstrom). The dummy atom I added at the end is<br>
>> > about<br>
>> > 31 A away from the closest water in the box. But if it is periodic,<br>
>> > shouldn't there be waters near the dummy too?<br>
>> ><br>
>> > On Wed, Mar 3, 2010 at 10:29 PM, Mark Abraham <<a href="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</a>><br>
>> > wrote:<br>
>> >><br>
>> >> On 4/03/2010 11:30 AM, Dian Jiao wrote:<br>
>> >>><br>
>> >>> Hi Gromacs users,<br>
>> >>><br>
>> >>> I was trying to compute minimum distance between groups in a cubic<br>
>> >>> water<br>
>> >>> box with g_mindist using periodic boundary condition. In order to test<br>
>> >>> this, I added one more "atom" which is far away from any of the other<br>
>> >>> atoms in the pdb file. The mindist between that atom and all the<br>
>> >>> waters<br>
>> >>> were computed. The output of g_mindist is 3.089281e+00. (the unit is<br>
>> >>> nm,<br>
>> >>> right?)<br>
>> >><br>
>> >> You haven't said how big your box is, or how far "far away" is, so we<br>
>> >> can't tell whether you think 3nm is too big, too small, etc.<br>
>> >><br>
>> >>> The manual shows that pbc is one of the option of g_mindist, but isn't<br>
>> >>> the default "yes"? I even tried with "-pbc" in the command, still did<br>
>> >>> not work. Can anyone tell me how to turn on PBC in g_mindist?<br>
>> >><br>
>> >> See g_mindist -h. The -pbc flag turns PBC on, -nopbc turns it off.<br>
>> >><br>
>> >> Mark<br>
>> >> --<br>
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>> --<br>
>> Tsjerk A. Wassenaar, Ph.D.<br>
>><br>
>> Computational Chemist<br>
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<br>
<br>
<br>
--<br>
Tsjerk A. Wassenaar, Ph.D.<br>
<br>
Computational Chemist<br>
Medicinal Chemist<br>
Neuropharmacologist<br>
--<br>
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</div></div></blockquote></div><br>