Hi all, I was trying to put a protein inside the membrane (generated by Charmm-Gui and I made some modification). I used "editconf -f protein.gro -o conf.gro -box (my box demension x y z)" and then "genbox -cp conf.gro -cs lipid_water_ion.gro -o box.gro" to remove the overlapped lipids. It looks fine in VWD, no overlap between protein and lipids occurred, but when I ran "grompp -f minim.mdp -c box.gro -p box.top -o box.tpr", it showed "Unknown cmap torsion between atoms 319 321 323 338 341". I try to built the box in several other ways, this problem kept occurring. So I searched for previous solution, and found the patch "0001-Fix-pdb2gmx-merge-cmap.patch" may fix the problem. However, I cannot use this patch because it needs to install in the source directory, but the Gromacs 4.5 I used is installed in our university system, I am not able to put the patch in the source directory.
So I would like to know, can I put the patch in my work directory to make it work? It asked "file to patch" if I put it in my work directory, so which file I need to patch? Or are there any other method can solve the problem for "Unknown cmap torsion between atoms"? I used charmm36 force field for all atom by the way. Thanks very much for your attention and assistance! Best, Ning -- 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.
