[gmx-users] Topology of Graphite Oxide
Hi users: I want to run a simulation of adsorption of protein on graphite oxide(GO) which is oxidized at random and is near 80% coverage by hydroxyl and epoxyl group. My first question is how to generate a topology filefor GO. Previous to search solution to this problem in this forum, I had tried to make a topology for GO use g_x2top with command: g_x2top -f input.pdb -nopbc -r outputname -o outputname. But g_x2top did not work fine(fine for prestine graphite) and gave error messages like "Can not find forcefield for atom .. " My second also is about definition of improper dihedral in opls-aa. Whether it is validate to assign a improper dihedral for a central sp2 carbon atom with three other bonded atoms no matter of what is type of other three atom? I have gotten (mentioned above) a topology file of pristine graphite for opls-aa with g_x2top(the command is similar to above), but the topology file did not include any improper dihedral. I will appreciated you for giving any advice. sincerely zhhxu PhD student Institute of Process Engineering, Chinese Academy of Sciences, Department of Biochemical Engineering. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] Re:Re: wrong bonds generate by g_x2top
Dear Justin: Thank you for reply. g_x2top worked correct as you suggested when I added "-nopbc" option. I have other questions about graphite simulation. The top/rtp file(opls-aa) generated by g_x2top missed improper dihedral term , to keep a carbon in plane, whether it is better to add the missing terms in topology file or need other corrections ? Thank you in advance! sincerely zhhxu PhD student Department of Biochemical Engineering Institute of Process Engineering Chinese Academy of Sciences -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] wrong bonded information in .top/.rtp file produced by g_x2top
hi all : I prepared top and rtp file for graphite using a command: g_x2top -f input.gro -r output -o output in GMX (V 4.5.5). A obvious mistake itp file is posted as below: [ bonds ] C1 C3776 1.420e-01 4.000e+05 C5 C3780 1.420e-01 4.000e+05 # for example，the distance between C1 and C3776 is at least 10 nm. the coordination is below: 1GRA C11 0.000 0.000 0.000 1GRAC3776 3776 0.000 10.068 0.000 Thanks in advance for any suggestion. sincrely， zhhxu PhD student Institute of Process Engineering, Chinese Academy of Sciences -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
