[gmx-users] A question to Justin about his helpful tutorial

khourshaeishargh at mech.sharif.ir khourshaeishargh at mech.sharif.ir
Sat Feb 20 12:12:37 CET 2016

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	Dear justin

	after finishing your tutorial, I tried to embed 1r2h protein into lipid
bilayer. when I tried to use pdb2gmx  via "gmx pdb2gmx -f
2rh1.pdb -o 2rh1_processed.gro -ignh -ter -water spc", it says :



	Select start terminus type for ASP-29

	 0: NH3+

	 1: NH2

	 2: None


	Start terminus ASP-29: None

	Select end terminus type for LEU-342

	 0: COO-

	 1: COOH

	 2: None


	End terminus LEU-342: None


	Program gmx, VERSION 5.0.5

	Source code file:
/home/ali/gromacs-5.0.5/src/gromacs/gmxpreprocess/pdb2top.cpp, line:


	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.


	I found a similar question in which you  replied it as below :

	You haven&#39;t added caps onto the input protein, you should expect to
get this error. In the tutorial, I build ACE and NH2 groups onto the
peptide to neutralize the termini. Since you haven&#39;t done this type
of modification, pdb2gmx will die because you have incomplete amides at
the ends of the chain. The "None" terminus instructs pdb2gmx to
not build additional H (in the case of NH2 or NH3+ termini) or O(H) (for
COO- and COOH). It doesn&#39;t make any chemical sense to use
"None" for non-capped protein chains.

	I don&#39;t grasp what specifically you  meant to say. Could you
please help me ? How should I naturalized the termini ? I really need


Ali khourshaei shargh (khourshaeishargh at mech.sharif.ir)
Department of Mechanical Engineering
Sharif University of Technology, Tehran, Iran



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