A follow up question to this, is it technically not possible to define an atomic distance constraint with just two atomic indices? <div><br /></div><div>If CP2K is capable of pointing out the wrongly specified molecule names, doesn't that mean CP2K already knows the molecules names that should correspond to the specified indices?<br /><br /></div><div>I apologize if this question sounded dumb.</div><div class="gmail_quote"><div dir="auto" class="gmail_attr">Ben siu 在 2025年7月6日 星期日中午12:47:09 [UTC+8] 的信中寫道：<br/></div><blockquote class="gmail_quote" style="margin: 0 0 0 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">Hi everyone, I am facing tremendous frustration with this problem. I am trying to constraint a COLVAR (defined in SUBSYS). The input manual mentioned to include either the MOLNAME or MOLECULE. <div><br></div><div>I started off using AMBER TOPOLOGY FILES and the initialization stages failed with "<span style="color:rgb(77,77,76);font-family:Menlo,monospace-fallback,monospace">| Error in constraints setup!</span></div><div><div style="color:rgb(77,77,76);font-family:Menlo,monospace-fallback,monospace"> | A constraint has been defined for a molecule type </div><div style="color:rgb(77,77,76);font-family:Menlo,monospace-fallback,monospace"> | but the atoms specified in the constraint and the atoms defined for </div><div style="color:rgb(77,77,76);font-family:Menlo,monospace-fallback,monospace"> | the molecule DO NOT match! </div><div style="color:rgb(77,77,76);font-family:Menlo,monospace-fallback,monospace"> | This could be very probable due to a wrong connectivity, or an error </div><div style="color:rgb(77,77,76);font-family:Menlo,monospace-fallback,monospace"> | in the constraint specification in the input file. </div><div style="color:rgb(77,77,76);font-family:Menlo,monospace-fallback,monospace"> | Please check it carefully! " </div><div style="color:rgb(77,77,76);font-family:Menlo,monospace-fallback,monospace"><br></div>After reading a related post on: <a href="https://groups.google.com/g/cp2k/c/IwsUR_RrDbk/m/YYO4fTrQUIwJ" target="_blank" rel="nofollow" data-saferedirecturl="https://www.google.com/url?hl=zh-TW&q=https://groups.google.com/g/cp2k/c/IwsUR_RrDbk/m/YYO4fTrQUIwJ&source=gmail&ust=1751863633417000&usg=AOvVaw2EIlzPFLdMvZyexZwsFZAL">https://groups.google.com/g/cp2k/c/IwsUR_RrDbk/m/YYO4fTrQUIwJ</a> , I did a fake run as suggested to dump the PSF and PDB and edited my PSF files to a unique SEGNAME (I decided to change it from MOL9 to SEGS). From the verbose output it looked like this: <span style="color:rgb(77,77,76);font-family:Menlo,monospace-fallback,monospace">1228. Molecule kind: _QM_SEGS Number of atoms: 33</span></div><span style="color:rgb(0,0,0)"><div style="color:rgb(77,77,76);font-family:Menlo,monospace-fallback,monospace"><div> Atom Atomic kind name </div><div> 1 P1 </div><div> 2 O29 </div><div> 3 O29 </div><div> 4 OS5 </div><div> 5 CI </div><div> 6 H113 </div><div> 7 H113 </div><div> 8 CT26 </div><div> 9 H136 </div><div> 10 OS7 </div><div> 11 CT21 </div><div> 12 H24 </div><div> 13 N*3 </div><div> 14 C1 </div><div> 15 H56 </div><div> 16 NB2 </div><div> 17 CB2 </div><div> 18 CA13 </div><div> 19 N23 </div><div> 20 H17 </div><div> 21 H17 </div><div> 22 NC2 </div><div> 23 CQ2 </div><div> 24 H52 </div><div> 25 NC5 </div><div> 26 CB6 </div><div> 27 CT28 </div><div> 28 H110 </div><div> 29 CT24 </div><div> 30 H126 </div><div> 31 OH5 </div><div> 32 HO3 </div><div> 33 OS4 </div><div> </div><div> The name was automatically generated: T </div><div> Number of molecules: 1 </div><div> Molecule list: 1228 </div><div> Number of bonds: 36 </div><div> Number of bends: 64 </div></div></span><div><br></div><div>Below are all the combinations I tried and still got the error: </div><div>MOLNAME: MOL9, _QM_MOL9, SEGS, _QM_SEGS, U (residue name –for the sake of testing)</div><div>MOLECULE: 1228, 9 (becuz MOL9) </div><div><br></div><div>Can anyone help and tell me what actually do these two keywords need? </div><div>Many Thanks</div></blockquote></div>
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