Hi Tsjerk,<br><br>Thanks for replying. I was going through the pdb format dcoument on the PDB webpage. I found that the box corresponds to the following:<br><br> a b(cos(gama)) c(cos(beta)) <br> 0 b(sin(gama)) c(cos(alpha) - cos(beta) cos(gama) / sin(gama)<br>
0 0 V/(ab sin(gama)) <br>where V = abc(1 - (cos(alpha))^2 - (cos(beta))^2 - (cos(gama))^2+ 2cos(alpha) cos(beta) cos(gama))^1/2<br><br>This corresponds to general form in representing these vectors. The following code also desolves to this form.<br>
<br>Thank you again.<br><br>Best,<br>Vishal<br><br>P.S. I thank all who have replied to this mail.<br><br><div class="gmail_quote">On Tue, Feb 2, 2010 at 3:44 PM, 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 Vishal,<br>
<br>
Here is a python function that generates a triclinic representation<br>
given a definition with lengths and angles. The argument L is a tuple<br>
or list containing the lengths and angles.<br>
<br>
def triclinic(L):<br>
B = [[0,0,0],[0,0,0],[0,0,0]]<br>
<br>
x, y, z, a, b, c = L[:6]<br>
<br>
B[0][0] = x<br>
if a == 90 and b == 90 and c == 90:<br>
B[1][1] = y<br>
B[2][2] = z<br>
else:<br>
a = a*pi/180<br>
b = b*pi/180<br>
c = c*pi/180<br>
B[1][0] = y*cos(c)<br>
B[1][1] = y*sin(c)<br>
B[2][0] = z*cos(b)<br>
B[2][1] = z*(cos(a)-cos(b)*cos(c))/sin(c)<br>
B[2][2] = sqrt(z*z-B[2][0]**2-B[2][1]**2)<br>
<br>
return B<br>
<br>
Hope it helps,<br>
<br>
Tsjerk<br>
<div><div></div><div class="h5"><br>
On Tue, Feb 2, 2010 at 9:23 PM, Erik Marklund <<a href="mailto:erikm@xray.bmc.uu.se">erikm@xray.bmc.uu.se</a>> wrote:<br>
> Hi,<br>
><br>
> Since any unit cell can be formulated as a triclinic cell, the monoclinic<br>
> cell is indeed supported. By definition it has two 90 degree angles and one<br>
> that is not 90 degrees. The box vectors can be of different lengths. You'll<br>
> have to do the math and reading yourself to find out how this translates to<br>
> a .gro box. The manual is your friend here.<br>
><br>
> Good luck,<br>
><br>
> Erik<br>
><br>
> Vishal Agarwal skrev:<br>
>><br>
>> Dear Justin,<br>
>><br>
>> Thanks for replying. The table mentions only a few unit cell type. I am<br>
>> using a monclinic unit cell. Do you know how these box vectors have been<br>
>> derived.<br>
>><br>
>> thanks<br>
>> vishal<br>
>><br>
>> On Tue, Feb 2, 2010 at 11:26 AM, Justin A. Lemkul <<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a><br>
>> <mailto:<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>>> wrote:<br>
>><br>
>><br>
>><br>
>> Vishal Agarwal wrote:<br>
>><br>
>> Dear gmx-users,<br>
>><br>
>> I am new to GROMACS. Can anyone tell me what does the last<br>
>> line in .gro file stands for ?<br>
>><br>
>> The manual mentions<br>
>> "box[X][X],box[Y][Y],box[Z][Z],<br>
>> box[X][Y],box[X][Z],box[Y][X],box[Y][Z],box[Z][X],box[Z][Y]"<br>
>><br>
>> Can anyone explain what each of these mean in terms of cell<br>
>> parameters ?<br>
>><br>
>><br>
>> The last line contains the box vectors. Specifics in terms of<br>
>> unit cell geometry are given in the manual, Table 3.1 and section<br>
>> 3.2.1.<br>
>><br>
>> -Justin<br>
>><br>
>> Thanks,<br>
>> vishal<br>
>><br>
>><br>
>> -- ========================================<br>
>><br>
>> Justin A. Lemkul<br>
>> Ph.D. Candidate<br>
>> ICTAS Doctoral Scholar<br>
>> MILES-IGERT Trainee<br>
>> Department of Biochemistry<br>
>> Virginia Tech<br>
>> Blacksburg, VA<br>
>> jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> <<a href="http://vt.edu" target="_blank">http://vt.edu</a>> | (540) 231-9080<br>
>> <a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
>><br>
>> ========================================<br>
>> -- gmx-users mailing list <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>
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>><br>
>><br>
>><br>
>><br>
>> --<br>
>> Regards<br>
>><br>
>> ***********************************************<br>
>> Vishal Agarwal<br>
>> Research Scholar<br>
>> University of Massachusetts, Amherst<br>
>> ***********************************************<br>
>> 'Your only obligation in any lifetime is to be true to yourself."<br>
>> ---Richard Bach<br>
><br>
><br>
> --<br>
> -----------------------------------------------<br>
> Erik Marklund, PhD student<br>
> Laboratory of Molecular Biophysics,<br>
> Dept. of Cell and Molecular Biology, Uppsala University.<br>
> Husargatan 3, Box 596, 75124 Uppsala, Sweden<br>
> phone: +46 18 471 4537 fax: +46 18 511 755<br>
> <a href="mailto:erikm@xray.bmc.uu.se">erikm@xray.bmc.uu.se</a> <a href="http://xray.bmc.uu.se/molbiophys" target="_blank">http://xray.bmc.uu.se/molbiophys</a><br>
><br>
> --<br>
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><br>
<br>
<br>
<br>
</div></div><font color="#888888">--<br>
Tsjerk A. Wassenaar, Ph.D.<br>
<br>
Computational Chemist<br>
Medicinal Chemist<br>
Neuropharmacologist<br>
</font><div><div></div><div class="h5">--<br>
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Please search the archive at <a href="http://www.gromacs.org/search" target="_blank">http://www.gromacs.org/search</a> before posting!<br>
Please don't post (un)subscribe requests to the list. Use the<br>
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Can't post? Read <a href="http://www.gromacs.org/mailing_lists/users.php" target="_blank">http://www.gromacs.org/mailing_lists/users.php</a><br>
</div></div></blockquote></div><br><br clear="all"><br>-- <br>Regards<br><br>***********************************************<br>Vishal Agarwal<br>Research Scholar<br>University of Massachusetts, Amherst<br>***********************************************<br>
'Your only obligation in any lifetime is to be true to yourself."<br> ---Richard Bach<br>