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; caret-color: rgb(0, 0, 0);">| Error in constraints setup!</span></div><div><div style="caret-color: rgb(0, 0, 0); color: rgb(77, 77, 76); font-family: Menlo, monospace-fallback, monospace;"> | A constraint has been defined for a molecule type </div><div style="caret-color: rgb(0, 0, 0); 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="caret-color: rgb(0, 0, 0); color: rgb(77, 77, 76); font-family: Menlo, monospace-fallback, monospace;"> | the molecule DO NOT match! </div><div style="caret-color: rgb(0, 0, 0); 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="caret-color: rgb(0, 0, 0); color: rgb(77, 77, 76); font-family: Menlo, monospace-fallback, monospace;"> | in the constraint specification in the input file. </div><div style="caret-color: rgb(0, 0, 0); color: rgb(77, 77, 76); font-family: Menlo, monospace-fallback, monospace;"> | Please check it carefully! " </div><div style="caret-color: rgb(0, 0, 0); color: rgb(77, 77, 76); font-family: Menlo, monospace-fallback, monospace;"><br /></div>After reading a related post on: https://groups.google.com/g/cp2k/c/IwsUR_RrDbk/m/YYO4fTrQUIwJ , 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; caret-color: rgb(0, 0, 0);">1228. Molecule kind: _QM_SEGS Number of atoms: 33</span></div><span style="caret-color: rgb(0, 0, 0); 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>
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