Ok. Thanks but I am doing a small test to make the .top file and .gro files of fresh 1K4C protein structure without removing anything but when I run my grommp command to minimize it as I asked earlier as well it says number of atoms in the .top are not equal to .top file and as you said that without adding any other molecule I just have to fix the [molecules] section, but it doesn't fix. here are some details of my .top file which I created on my own after getting the 1K4C.itp file. I got 1K4C.itp file something like this..
grep -A 1 1K4C 1K4C.txt > 1K4C.seq (This generates 1K4C.seq) dsspcmbi 1K4C.pdb 1K4C.dssp (gives 1K4c.dssp) dssp2ssd.py 1K4C.dssp -o 1K4C.ssd (this gives 1K4C.ssd) seq2itp.pl 1K4C.seq 1K4C.ssd > 1K4C.itp My topology file looks like this ; Include forcefield parameters #include "martini_v2.1.itp" ; Include protein #include "1K4C.itp" [ system ] ; Name Membrane Protein [ molecules ] ; compound # mols Protein 1 and after that I produce my 1K4C.gro file from genbox or editconf and then when i run the command grommp it says that number of atoms in .gro file are unequal to .top file. Since I am doing the simulation in vacuum I cannot add anything else. Don't know how to proceed. Thanks, Sunny On Tue, Aug 18, 2009 at 7:00 PM, Justin A. Lemkul <[email protected]> wrote: > > > sunny mishra wrote: > >> Hi all, >> >> Is there anyway I can generate the .gro file from .top file without using >> the command pdb2gmx and editconf? >> >> > A .top file is a topology - atomic descriptions; a .gro is a coordinate > file. They are unrelated and therefore cannot be inter-converted. > > -Justin > > >> ------------------------------------------------------------------------ >> >> _______________________________________________ >> gmx-users mailing list [email protected] >> 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 [email protected]. >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php >> > > -- > ======================================== > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > ======================================== > _______________________________________________ > gmx-users mailing list [email protected] > 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 [email protected]. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php >
_______________________________________________ gmx-users mailing list [email protected] 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 [email protected]. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
