[gmx-users] pdb2gmx peptide nanotube

[Farzane Abasi]

*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*