$ ../protein.exe

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  ###                                                                      ###
 ###            TINKER  ---  Software Tools for Molecular Design            ###
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 ##                        Version 8.4  February 2018                        ##
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 ##               Copyright (c)  Jay William Ponder  1990-2018               ##
 ###                           All Rights Reserved                          ###
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  ### Special version for Windows (x86)                                    ###
  ### compiled by Alan Liska & Veronika Ruzickova                          ###
  ### on March 21, 2019                                                    ###
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 Enter Name to be Used for Output Files :  test2

 Enter Title :  test2

 Enter Potential Parameter File Name :  ../../params/amoeba04

 Enter One Residue Name per Line as the Standard Three-Letter Code, then
 Phi Psi Omega (3F), Chi Angles (4F), then Disulfide Partner if CYX (I),
 and D/L Chirality as Desired (A1)

 If Only Residue Names are Entered, the Default is to Build an Extended
 Conformation Using L-Amino Acids and Zwitterionic Termini

 Regular Amino Acids:  GLY, ALA, VAL, LEU, ILE, SER, THR, CYS, CYX, PRO,
 PHE, TYR, TRP, HIS, ASP, ASN, GLU, GLN, MET, LYS, ARG, ORN, AIB

 Alternative Protonation States:  CYD, TYD, HID, HIE, ASH, GLH, LYD

 N-Terminal Cap Residues:  H2N=Deprotonated, FOR=Formyl, ACE=Acetyl,
                           PCA=Pyroglutamic Acid
 C-Terminal Cap Residues:  COH=Protonated, NH2=Amide, NME=N-MethylAmide

 Use Residue Name=MOL to Start a New Chain, and Use <CR> to End Input

 Enter Residue   1 :  ALA

 Enter Residue   2 :  GLY

 Enter Residue   3 :

 Cyclize the Polypeptide Chain [N] :  N