On Mon, Nov 25, 2013 at 4:53 AM, sunita gupta <sunita....@gmail.com> wrote:
> Hello everyone, > > I am trying to do implicit MD of protein-ligand complex using > amberff99sb-ildn. > I am getting following error at grompp minimization step > > *GB parameter(s) missing or negative for atom type 'c3'GB parameter(s) > missing or negative for atom type 'n2'GB parameter(s) missing or negative > for atom type 'ce'GB parameter(s) missing or negative for atom type 'os'GB > parameter(s) missing or negative for atom type 'cl'GB parameter(s) missing > or negative for atom type 'h1'GB parameter(s) missing or negative for atom > type 'hc'GB parameter(s) missing or negative for atom type 'ha'GB > parameter(s) missing or negative for atom type > 'hn'-------------------------------------------------------Program grompp, > VERSION 4.5.5Source code file: grompp.c, line: 1123Fatal error:Can't do GB > electrostatics; the implicit_genborn_params section of the forcefield is > missing parameters for 9 atomtypes or they might be negative.For more > information and tips for troubleshooting, please check the GROMACSwebsite > at http://www.gromacs.org/Documentation/Errors > <http://www.gromacs.org/Documentation/Errors>* > > After reading earlier archive I tried -g disambguate option of acpype, but > the atomtypes are still case sensitive. Also I tried to modify the > gbsa.infile by adding these atomtypes with default vanderwalls radii > and chaged > two atomtypes in lig.itp by HA and N2 ( which is provided in gbsa.in), but > the problem is still the same.. > GB parameter(s) missing or negative for atom type 'HA' > > GB parameter(s) missing or negative for atom type 'N2' > > GB parameter(s) missing or negative for atom type 'c3' > > GB parameter(s) missing or negative for atom type 'ce' > > GB parameter(s) missing or negative for atom type 'os' > > GB parameter(s) missing or negative for atom type 'cl' > > GB parameter(s) missing or negative for atom type 'h1' > > GB parameter(s) missing or negative for atom type 'hc' > > GB parameter(s) missing or negative for atom type 'hn' > > I don't understand why its again complaining about HA and N2, even if it is > present in lig.itp. > > Their presence in lig.itp is irrelevant; it's the fact that parameters are not assigned for these atom types in gbsa.itp in the [implicit_genborn_params] directive. -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.
