On 1/15/14, 10:06 AM, jwill...@andrew.cmu.edu wrote:
Hello, I was under the impression that pdb2gmx was supposed to referance the force fields as defined in oplsaa.ff/forcefield.itp, but it doesn't seem to be for me. To double check, I removed all force field parameters from forcefield.itp and pdb2gmx still ran and got the same result as before. How do I make pdb2gmx referance oplsaa.ff/forcefield.itp?
pdb2gmx doesn't do much of anything with forcefield.itp. You tell it which force field you want to use, then it makes use of lots of files in that directory (see the manual for the list). Most significant is the .rtp file. The #include statement for the force field is then simply written to the .top based on your selection.
-Justin -- ================================================== Justin A. Lemkul, Ph.D. 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 ================================================== -- 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.
