*Dear Gromacs users,* I am trying to simulate a peptide nanutube composed by 8 cyclics.When I execute pdb2gmx with the options -missing and -ter (selecting manually None), as I have seen in the Gromacs list, I get this error: pdb2gmx -f tube.pdb -ter -missing -ignh8 out of 8 lines of specbond.dat converted successfullySelect start terminus type for LEU-1 0: NH3+ 1: NH2 2: 5TER 3: None3Start terminus LEU-1: NoneSelect end terminus type for GLN-10 0: COO- 1: COOH 2: CT2 3: 3TER 4: None4End terminus GLN-10: None -------------------------------------------------------Program gmx pdb2gmx, VERSION 5.1.2Source code file: /build/gromacs-z6bPBg/gromacs-5.1.2/src/gromacs/gmxpreprocess/pdb2top.cpp, line: 1088 Fatal error:There is a dangling bond at at least one of the terminal ends. Fix your coordinate file, add a new terminal database entry (.tdb), or select the proper existing terminal entry.For more information and tips for troubleshooting, please check the GROMACSwebsite at http://www.gromacs.org/Documentation/Errors-------------------------------------------------------Could anyone help to solve this, please? Best wishes, DARYA.
-- *Farzane Abasi, Ph.D. Student (Biophysics)* *School of Biological Sciences* *Trabiat Modares University (TMU), Tehran, Iran* *Cellular: +98(913)736-3079* -- 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.
