Dear gromacs users Previously, I simulated collagen triple helix chains, (GLY-PRO-HYP)n using Amber99sb-ILDN forcefield. When I processed pdb structures with pdb2gmx, I only obtained GLY in the N termini properly, and HYP was not processed(it was treated like HYP, not terminal HYP) since there was no HYP library describing C termini. Therefore, I added CHYP data in library and everything was fine.
Now I am trying to simulate infinite collagen triple chains, (GLY-PRO-HYP)n where GLY in N-terminus is connected to the HYP in C-terminus through the periodic boundary condition. So, I would like to process structures with pdb2gmx and wanted to treat NGLY and CHYP in termini as a GLY and HYP. So I removed CHYP library I added before, and removed NGLY library too. Without NGLY library, However, pdb2gmx does not work well and says there is dangling bond so investigate *.rtp or *.tdb. Without CHYP library, pdb2gmx worked well and just processed CHYP like HYP, Does anyone know why this error occurs in case of N-termini? Thanks for you advice in advance. Sincerely, Sangeun Jee -- Post Doctoral Researcher School of Materials Science and Engineering Georgia Institute of Technology -- 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 [email protected].
