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