On 1/22/14, 1:06 PM, Sidath Wijesinghe wrote:
Justin, i was able to generate the .top file for 3 monomers by making the corresponding .rtp entry. below is a segment of my .rtp entry and thr .pdb file i used. .rtp entry for first few atoms out of 208 [ UNK ] [ atoms ] C1 opls_240 0 1 C2 opls_145 -0.12 1 C3 opls_240 0 1 C4 opls_240 0 1 C5 opls_158 -0.12 1 C6 opls_158 -0.12 1 C7 opls_158 -0.12 1 C8 opls_158 -0.12 1 C9 opls_158 -0.12 1 C10 opls_158 -0.12 1
I can almost guarantee that charge group is inappropriately large. Charge groups generally have no more than 3-4 atoms (see the manual).
[ bonds ] C1 C2 C1 C13 C1 C82 C2 C3 C2 H28 C3 C4 C3 C5 C4 C11 C4 C21 C5 C6 C5 H29 and so on.... segment of my .pdb used. ATOM 1 C1 UNK 1 -0.3884 0.71623 0.01741 1.00 0.00 UNK ATOM 2 C2 UNK 1 0.52009 1.96858 0.02142 1.00 0.00 UNK ATOM 3 C3 UNK 1 2.05261 1.8016 0.02832 1.00 0.00 UNK ATOM 4 C4 UNK 1 2.67378 0.39693 0.04493 1.00 0.00 UNK ATOM 5 C5 UNK 1 3.00381 3.01293 0.02021 1.00 0.00 UNK ATOM 6 C6 UNK 1 2.43967 4.44371 0.06547 1.00 0.00 UNK ATOM 7 C7 UNK 1 3.74954 5.25409 0.04830 1.00 0.00 UNK ATOM 8 C8 UNK 1 3.66193 6.78984 0.08175 1.00 0.00 UNK ATOM 9 C9 UNK 1 5.14612 7.20376 0.05800 1.00 0.00 UNK ATOM 10 C10 UNK 1 5.41193 8.7194 0.08617 1.00 0.00 UNK ATOM 11 C11 UNK 1 4.20533 0.24061 0.06162 1.00 0.00 UNK ATOM 12 C12 UNK 1 5.73704 0.08685 0.07550 1.00 0.00 UNK ATOM 13 C13 UNK 1 0.24354 -0.6927 0.01957 1.00 0.00 UNK ATOM 14 C14 UNK 1 -0.6215 -1.9681 0.00425 1.00 0.00 UNK ATOM 15 C15 UNK 1 -2.1484 -1.7855 0.06322 1.00 0.00 UNK i was able to get the .gro and .top file using pdb2gmx after that i was using grompp but i got an error message as follows. ERROR 254 [file topol.top, line 1941]: No default Ryckaert-Bell. types ERROR 255 [file topol.top, line 1942]: No default Ryckaert-Bell. types ERROR 256 [file topol.top, line 1943]: No default Ryckaert-Bell. types i was reading the gmx_users blogs and it specifies that i need to manually enter the parameters that have errors. i am not clear with that. could you please tell me what i need to do here. ( when i look the lines regarding the errors they are pointing out the diheadrals)
You need to check those lines for what the atom types are for those atoms. Parameters are not present in ffbonded.itp for that sequence of atoms so you need to add suitable parameters.
-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.