Hi, I have a small problem, I have a relatively big ligand (ca 1200Da) and I want to fuse him (the fragments exist as rtp). And I thought that the online servers to calculate could be not good enough for that ligand. For that reason I have chosen the specbond.dat wa. Now I am able to fuse the part Non-Protein, Non-Protein and I am able to make a bond Protein-Protein. This gives a correct file and the bond of spec-bond is included.
But now I try the same thing with the same ligand (means also the same rtp entries with Non-Protein and Protein: Linking LYS-3 N-9 and PLI-0 C7-117... Linking LYS-8 N-35 and PLI-0 C7-141... Linking LEU-1 C-44 and LYS-1 NZ-60... Linking GALB-0 O1-101 and PLI-0 C1-111... Linking GALB-0 O1-125 and PLI-0 C1-135... Start terminus LYS-3: NH3+ End terminus ILE-14: COO- ------------------------------------------------------- Program pdb2gmx_mpi, VERSION 4.6.5 Source code file: /usr/local/gromacs-4.6.5/src/kernel/pdb2top.c, line: 960 Fatal error: Residues in one molecule have a different 'bonds' type: 2 and 1 For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors ------------------------------------------------------- "With a Lead Filled Snowshoe" (F. Zappa) I searched long and it's still not clear to me, why this bonds type error is coming... And it's really only if I try to combine non-protein and protein rtp entries. If I do with the same method any other combination, then is there no problem... Someone knows, why bonds type occurs? P.S. PLI is myself build with ATB Server and translated to rtp. But the error also occurs if I only take Galactose and Protein for testing reasons... Ok, clear, the code/method on line 960 compares two values and they are different, but this helps me not if I don't know which value is not fitting... Thank you for your answers. Or suggestions to solve the problem... -- View this message in context: http://gromacs.5086.x6.nabble.com/Fuse-Protein-and-non-Protein-Part-of-Ligand-tp5015894.html Sent from the GROMACS Users Forum mailing list archive at Nabble.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.