Dear all, I'd like to use the gromacs analysis tool to analyse a simulation performed with charmm. I installed the latest gromacs version (5.0.4), in which both .dcd trajectories and all the files read also by vmd should be readable. After that, the trajectory is correctly processed by gromacs, but I've troubles with the analysis tools that need .tpr files. As suggested in some previous posts, I've generated a fake file .top with vmd, useful to produce a new .tpr suitable for the analysis. I also installed the charmm36 forcefield in the gmx top directory (the same that I used in the simulation). When I use grompp to generate a .tpr, I get this error:
Fatal error: Unknown cmap torsion between atoms 5 7 9 22 24 Among the possible solutions I found the use of this patch, but this was concerning an older vs of gromacs: “0001-Fix-pdb2gmx-merge-cmap.patch”, so I skipped it during installation. I do not understand if this error it's a matter of forcefield or it depends on something else. Does anyone could help me to figure-out the origin of the error and how to fix the problem? Also pdb2gmx is not working because some atoms are not found in the forcefield (such as CAY, used by charmm for methylated methionine). Manipulating the forcefield would fix both the problems? In this case how should I proceed? I'd really appreciate any suggestion! Thank you very much in advance! Chiara -- 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 [email protected].
