On 7/29/14, 2:45 PM, John Doe wrote:
Hi, I'm attempting to simulate "polyethylene" using OPLS (I'm using Gromacs 5.0.1-dev). I'm using the files from: https://www.mail-archive.com/gmx-users@gromacs.org/msg19683.html I have moved the OPLS force field directory to my working directory and placed "ffoplsaa.rtp" and "ffoplsaa.hdb" in the OPLS directory. I use pdb2gmx (selecting the option for OPLS in my folder) to produce the gro and top files """ gmx pdb2gmx -f polyethylene.pdb -o PE_processed.gro """ This works fine. I think enlarge the simulation box: """ gmx editconf -f PE_processed.gro -o PE_bigBox.gro -bt cubic -c -d 2.0 """ Again, works fine. I then move on to energy minimize using the mdp file from: http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/Files/minim.mdp However, when I run grompp: gmx grompp -f minim.mdp -c PE_bigBox.gro -p topol.top -o PE_minim.tpr I get the following error: """ ERROR 1 [file topol.top, line 162]: No default Proper Dih. types ERROR 2 [file topol.top, line 163]: No default Proper Dih. types ERROR 3 [file topol.top, line 164]: No default Proper Dih. types ERROR 4 [file topol.top, line 165]: No default Proper Dih. types ERROR 5 [file topol.top, line 166]: No default Proper Dih. types """ I'm not quite sure why I'm getting this error because the dihedral are defined in OPLS. Take for instance ERROR 1. This error correlates to the dihedral "HC-CT-CT-CT", however, in the OPLS bonded parameters file, the dihedral is written out as "CT-CT-CT-HC", so I'm not sure why grompp is not processing this. Does this dihedral need to be reversed? Then ERROR 2 corresponds to "CT-CT-CT-CT" which is defined in the bonded parameters (file "ffbonded.itp"). So I'm not really sure what's going on.
Something doesn't add up. Dihedrals can be interpreted in forward or reverse order, so that doesn't matter; the fact that CT-CT-CT-CT fails is indicative of some underlying problem with the topology. If you can post the topology for download somewhere, it will be easier to diagnose.
-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.
