On 5/26/14, 2:20 PM, shivangi nangia wrote:
Hello, I was able to convert my coarse grained system to all-atom using the backward script. However, it (Mapping folder) only had option for charmm36. I have an all-atom .gro file and .top file for charmm36 but I need t run my simulations with charmm27. Doing pdb2gmx with all-tom .gro file runs into error which I believe is for mismatch in atom types between charmm36 and 27.
Providing us with the actual error message is vastly more helpful.
Also,on using the command (./initram.sh -f system.gro -f system_aa.top -po backmapped.top -from martini -to charmm27) handled the protein part of the system but ran into error for POPC, but changing -from martini -to charmm36 successfully converted to all atom.
If you need to use a different force field, you need to generate a new topology under that force field. CHARMM36 is superior to other versions of the force field, especially for lipids, so take that into consideration.
-Justin -- ================================================== Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul ================================================== -- 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.
