Dear Justin Thank you for your reply I noticed my problem ( the reason was topolgen.pl name in my directory, it is named topologen_1.1.pl in the working directory) I generated my ligand topology but got this : No output type specified. Using default type of .top Unknown atom type: N 13 with 2 bonds - cannot assign atom type. Using default H type for atom 16. Using default H type for atom 26. Using default H type for atom 31. Using default H type for atom 38. Using default H type for atom 39. Using default H type for atom 40. Using default H type for atom 41. Unknown atom type: N 42 with 2 bonds - cannot assign atom type. Using default H type for atom 47. Using default H type for atom 48. Using default H type for atom 49. Using default H type for atom 50. Using default H type for atom 51. Using default H type for atom 52.
******************************************************** WARNING: Net charge on the molecule is -2.781 You will need to make corrections to the output topology ******************************************************** TopolGen, version 1.1_dev (10/14/2009) complete. Output topology has been written. An attempt has been made to assign charges and atom types based on existing functional groups, but they may not be correct. No charge calculations or other parameterization calculations have been done. Guesses have been made for charge groups. Please inspect and correct the topology before using it in any simulations. The author of the script does NOT guarantee accuracy or usability of any of the content; TopolGen was written as a convenience for outputting a skeleton topology, and nothing more. the N13 atom connected to C with double bond. it sounds topolgen can not identify N atom in 2 bonds with C . would you please help me to figure out this problem thans in advanceFarial On Sunday, July 15, 2018, 5:23:41 PM GMT+4:30, Justin Lemkul <jalem...@vt.edu> wrote: On 7/15/18 1:38 AM, farial tavakoli wrote: > Dear Justin > > But I copied & pasted topolgen and perl5 folders in the working directory. > and faced the mentioned error. > > Can't open perl script "topolgen.pl": No such file or directory > I dont know how I should figure out this problem. The problem is still the same: there's nothing called "topolgen.pl" in the working directory. List your files, you'll see it's called something else. > Which one of all-atom force fields will you choose to run a simulation on a > complex with small molecule, if you want to calculate binding energy using > G_MMPBSA ?I really need your guidance . Presumably any of them, but I don't do such calculations. -Justin -- ================================================== Justin A. Lemkul, Ph.D. Assistant Professor Virginia Tech Department of Biochemistry 303 Engel Hall 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.thelemkullab.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. -- 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.