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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 2 Start terminus ASP-29: None Select end terminus type for LEU-342 �0: COO- �1: COOH �2: None 2 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: 1091 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'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'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't make any chemical sense to use "None" for non-capped protein chains. I don't grasp what specifically you� meant to say. Could you please help me ? How should I naturalized the termini ? I really need it. sincerely Ali khourshaei shargh (khourshaeisha...@mech.sharif.ir) Department of Mechanical Engineering Sharif University of Technology, Tehran, Iran �
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