Hi Justin Its problem with the waters I think. I found conflict in water atom names:
charmm36-jan2014.ff/tip3p.itp: 1 OT 1 SOL OW 1 -0.834 2 HT 1 SOL HW1 1 0.417 3 HT 1 SOL HW2 1 0.417 charmm36-jan2014.ff/merged.itp [ TIP3 ] [ atoms ] OH2 OT -0.834 0 H1 HT 0.417 1 H2 HT 0.417 2 In PDB from charmgui its OH2,H1,H2. I changed names in charmm36-jan2014.ff/tip3p.itp as in merged.rtp but still I get same error. On Mon, Mar 3, 2014 at 5:46 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 3/3/14, 10:57 AM, gromacs query wrote: > >> Hi All >> >> I am trying to use charmm36 (charmm36-jan2014 from charmm website) with >> popc membrane built using charmm-gui (have water and ions). >> >> I used commands as follows: >> >> pdb2gmx -f step5_assembly.pdb -o popc.gro -water tip3p -ff >> charmm36-jan2014 >> editconf -f popc.gro -o popc_box.gro -c -d 0.0 >> grompp -f minim.mdp -c popc_box.gro -p topol.top -o em.tpr >> >> I get this error: (so many) >> ERROR 11520 [file topol.top, line 184419]: >> No default U-B types >> >> Where are UB for charmm36? >> >> > This shouldn't happen. Can you please identify what atoms are causing the > failure? It may help to simplify by working only with a single lipid > rather than a full membrane. > > -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. > -- 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.