[CP2K-user] [CP2K:21619] Re: CONSTRAINT WARNING WITH PSF/PDB

[Ben siu]

A follow up question to this, is it technically not possible to define an 
atomic distance constraint with just two atomic indices? 

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?

I apologize if this question sounded dumb.
Ben siu 在 2025年7月6日 星期日中午12:47:09 [UTC+8] 的信中寫道：

> 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. 
>
> I started off using AMBER TOPOLOGY FILES and the initialization stages 
> failed with "| Error in constraints setup!
> | A constraint has been defined for a molecule type 
> | but the atoms specified in the constraint and the atoms defined for 
> | the molecule DO NOT match! 
> | This could be very probable due to a wrong connectivity, or an error 
> | in the constraint specification in the input file. 
> | Please check it carefully! " 
>
> 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: 1228. Molecule kind: _QM_SEGS Number of 
> atoms: 33
> Atom Atomic kind name 
> 1 P1 
> 2 O29 
> 3 O29 
> 4 OS5 
> 5 CI 
> 6 H113 
> 7 H113 
> 8 CT26 
> 9 H136 
> 10 OS7 
> 11 CT21 
> 12 H24 
> 13 N*3 
> 14 C1 
> 15 H56 
> 16 NB2 
> 17 CB2 
> 18 CA13 
> 19 N23 
> 20 H17 
> 21 H17 
> 22 NC2 
> 23 CQ2 
> 24 H52 
> 25 NC5 
> 26 CB6 
> 27 CT28 
> 28 H110 
> 29 CT24 
> 30 H126 
> 31 OH5 
> 32 HO3 
> 33 OS4 
> The name was automatically generated: T 
> Number of molecules: 1 
> Molecule list: 1228 
> Number of bonds: 36 
> Number of bends: 64       
>
> Below are all the combinations I tried and still got the error: 
> MOLNAME: MOL9, _QM_MOL9, SEGS, _QM_SEGS, U (residue name –for the sake of 
> testing)
> MOLECULE: 1228, 9 (becuz MOL9) 
>
> Can anyone help and tell me what actually do these two keywords need? 
> Many Thanks
>

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