[CP2K:3316] Constraint warning with AMBER PDB file

Teodoro Laino teodor... at gmail.com
Wed Jun 22 07:06:29 UTC 2011

On Jun 22, 2011, at 8:44 AM, marco.stenta wrote:

> The problem is that I have 47883 water molecules: do I have to repeat this CONSTRAINT  section (or the &G3X3 subsection ) 50 thousand time? the input would be pretty big.
> Is there a clever way to SHAKE water molecules in my case?
yes (see below)

> you write in your previous answer 
> MOLECULE 1..15
> but from the manual I understand MOLECULE takes only one integer: what does your line mean? can I specify for a range instead then for a single molecule?
that's right..  I'll see how tough it is to convert this keyword to a list..

> Is it possible to have the code recognizing a MOLNAME also when one uses an amber topology?
not easily, because AMBER topology has to be heavily digested unfortunately and molnames have to be changed.. Clearly one can always hack this procedure, but it is not my intention do so at the moment..

> I am forced to use amber topology as I did not find the ambertocharmm converter (leap2fist ?) anymore and I have to shake water, of course.
I decided to embed the leap2fist in cp2k: less maintenance.. you can still dump the PSF and PDB after digestion and use them to re-run cp2k with the proper styles..
At this stage you can decide to give the name you like more to the residues in the PSF, and then use just 1 constraint for WATER (assuming all water have the molname WATER).

> More in general: what do you mean by "molecule"?
> each residue of a protein is assigned to a "molecule": what is the  meaning of that?
> what if I set it to FALSE?
PARA_RES distributes the residues instead of molecules.

> I get the term molecule has nothing to do with its chemical meaning, but my protein part is composed by more than one sub-units: does that conflicts with PARA_RES FALSE?
> Then I get some strange molecules as well like 
>      1. Molecule kind: _QM_MOL0                  Number of atoms:          10657
> this is not the QM part, nor the QM + link and I am lost 

no input.. no idea..

> thanks for the help
> m
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