---------- Forwarded message ---------- From: sunita gupta <sunita....@gmail.com> Date: Mon, Nov 25, 2013 at 3:23 PM Subject: Can't do GB electrostatics; the implicit_genborn_params section of the forcefield is missing parameters for 9 atomtypes or they might be negative. To: gmx-us...@gromacs.org
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. Kindly guide in tackling this problem. Thanks in advance -- -- SUNITA GUPTA Senior Research Fellow Bioinformatics Centre Jawaharlal Nehru University New Delhi- 110067 Email- sunita....@gmail.com -- -- SUNITA GUPTA Senior Research Fellow Bioinformatics Centre Jawaharlal Nehru University New Delhi- 110067 Email- sunita....@gmail.com -- 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.