Hello GROMACS community, I am having problems maintaining the shape of my system box after using ParmEd to convert from Amber to Gromacs format.
I parameterized a system with AmberTools (peptide solvated in an octahedral box). I then converted the Amber files (.inpcrd and .prmtop) to GROMACS format (.gro and .top) using ParmEd. I used VMD to look at the system, and it looks ok (peptide still centered in an octahedral box). ( http://i1380.photobucket.com/albums/ah185/cmvander/parmed_zpssaq6ldnb.png) Next I did an energy minimization in GROMACS. VMD displayed the resulting .gro file as a triclinic box and the peptide is no longer centered. ( http://i1380.photobucket.com/albums/ah185/cmvander/minimized_zpsekznpl3w.png ) I think that the system really is still an octahedral box because I can see the octahedral box boundaries within the triclinic box. I overlaid both systems and the protein is in the same spot ( http://i1380.photobucket.com/albums/ah185/cmvander/image_overlay_zpsepfpqkvl.png). Also I got reasonable minimization energies. Steepest Descents converged to Fmax < 1000 in 337 steps Potential Energy = -3.1393012e+05 Maximum force = 9.0675385e+02 on atom 363 Norm of force = 3.5674736e+01 Am I just doing something wrong to cause VMD to display my system incorrectly, or is there a more serious issue? Either way, I’d be happy to know how to fix it! Thanks in advance for any advice! I really appreciate it! Crystal Some extra information------- The last line of the AMBER .inpcrd file: 68.4778914 68.4778914 68.4778914 109.4712190 109.4712190 109.4712190 The last line of the .gro file from ParmEd conversion: 6.84779 6.45616 5.59120 0.00000 0.00000 -2.28260 0.00000 -2.28260 -3.22808 The last line of the em.gro file resulting from energy minimization: 6.84779 6.45616 5.59120 0.00000 0.00000 -2.28260 0.00000 -2.28260 -3.22808 I tried using editconf as suggested here ( http://manual.gromacs.org/programs/gmx-editconf.html), but I don’t think this is the right track for my problem. Minimization failed when I tried to use the structure I made by doing this. “To convert a truncated octrahedron file produced by a package which uses a cubic box with the corners cut off (such as GROMOS), use: *>>>*gmx editconf -f in -rotate 0 45 35.264 -bt o -box veclen -o out where veclen is the size of the cubic box times sqrt(3)/2.” -- Crystal M. Vander Zanden, Ph.D. ASERT Postdoctoral Fellow (IRACDA) University of New Mexico, Albuquerque -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.