<html><body bgcolor="#FFFFFF"><div>These are two different problems:</div><div><br></div><div>1) since you use amber topologies you should never handle mm types, the only case would be for specifying RADIUS in QM/MM. In this case you can dump a PDB file where the new kinds are written and start from there..</div><div>In the future I may think about assigning RADIUS to elements instead of kinds but for the time being, unfortunately, there is (for amber only) a little overhead.</div><div><br></div><div>2) the error you see is related to QS. you didn't specify the KIND section in the subsys for the QM atoms. These kinds have nothing to do with amber but it was you to specify them with the QM_KINDS in the QMMM section.</div><div><br>---------------------------------------------<div>Teodoro Laino</div><div>Zurich Switzerland</div><div><br></div><div>Contact info:</div><div>Tel.: <a href="http://www.jajah.com/Teo"><a href="http://www.jajah.com/Teo">http://www.jajah.com/Teo</a></a><span class="Apple-style-span" style="-webkit-composition-fill-color: rgba(175, 192, 227, 0.231373); -webkit-composition-frame-color: rgba(77, 128, 180, 0.231373); "></span></div><div><span class="Apple-style-span" style="-webkit-composition-fill-color: rgba(175, 192, 227, 0.231373); -webkit-composition-frame-color: rgba(77, 128, 180, 0.231373); ">E-mail: <a href="mailto:teo...@laino.eu"><a href="mailto:teo...@laino.eu">teo...@laino.eu</a></a></span></div><div><span class="Apple-style-span" style="-webkit-composition-fill-color: rgba(175, 192, 227, 0.231373); -webkit-composition-frame-color: rgba(77, 128, 180, 0.231373);"> <a href="mailto:teodor...@gmail.com"><a href="mailto:teodor...@gmail.com">teodor...@gmail.com</a></a></span></div><div>---------------------------------------------</div></div><div><br>On 10 Jun 2009, at 17:25, Marius Retegan <<a href="mailto:marius.s...@gmail.com">marius.s...@gmail.com</a>> wrote:<br><br></div><div></div><blockquote type="cite"><div>So if I want to use amber topologies can you think of an "easy" method for preparing the input files for QM/MM calculations?<br>Also even if I don't assign any kinds to mm atoms I get this error message:<br><br>
*<br> *** ERROR in read_atomic_kind (MODULE atomic_kind_types) ***<br> *<br><br><br> *** No &KIND section was possible to associate to the atomic kind <O>. ***<br> *** The KIND section were also scanned for the corresponding element <O> ***<br>
*** and for the DEFAULT section but no match was found. Check your input ***<br> *** file! ***<br><br><br> *** Program stopped at line number 1538 of MODULE atomic_kind_types ***<br>
<br> ===== Routine Calling Stack =====<br><br> 5 read_atomic_kind<br> 4 read_atomic_kind_set<br> 3 quickstep_create_force_env<br> 2 qmmm_create_force_env<br> 1 CP2K<br>
CP2K| Abnormal program termination, stopped by process number 0<br><br>Thanks<br>Marius<br><br><div class="gmail_quote">On Wed, Jun 10, 2009 at 4:24 PM, Teodoro Laino <span dir="ltr"><<a href="mailto:teodor...@gmail.com"><a href="mailto:teodor...@gmail.com">teodor...@gmail.com</a></a>></span> wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"><div bgcolor="#FFFFFF"><div>Because for CP2K a kind has a specific charge. Same kinds have same charge. For amber the charge has nothing to do with the kinds, i.e. same kinds can have different charges.<div class="im">
<br><br>---------------------------------------------<div>Teodoro Laino</div><div>Zurich Switzerland</div><div><br></div><div>Contact info:</div><div>Tel.: <a href="http://www.jajah.com/Teo" target="_blank"></a><a href="http://www.jajah.com/Teo" target="_blank"><a href="http://www.jajah.com/Teo">http://www.jajah.com/Teo</a></a><span></span></div>
<div><span>E-mail: <a href="mailto:teo...@laino.eu" target="_blank"></a><a href="mailto:teo...@laino.eu" target="_blank"><a href="mailto:teo...@laino.eu">teo...@laino.eu</a></a></span></div><div><span> <a href="mailto:teodor...@gmail.com" target="_blank"></a><a href="mailto:teodor...@gmail.com" target="_blank"><a href="mailto:teodor...@gmail.com">teodor...@gmail.com</a></a></span></div>
<div>---------------------------------------------</div></div></div><div><div></div><div class="h5"><div><br>On 10 Jun 2009, at 16:12, Marius Retegan <<a href="mailto:marius.s...@gmail.com" target="_blank"><a href="mailto:marius.s...@gmail.com">marius.s...@gmail.com</a></a>> wrote:<br>
<br></div><div></div><blockquote type="cite"><div>But why can't the atomic kinds be assigned from the amber parameter file instead of being automatically generated?<br><br><div class="gmail_quote">On Wed, Jun 10, 2009 at 4:09 PM, Teodoro Laino <span dir="ltr"><<a href="mailto:teodor...@gmail.com" target="_blank"></a><a href="mailto:teodor...@gmail.com" target="_blank"><a href="mailto:teodor...@gmail.com">teodor...@gmail.com</a></a>></span> wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"><div bgcolor="#FFFFFF"><div>No, for varius reasons of compatibility between AMBER and CHARMM (which is the FF natively supported) this is not possible.<br>
<br>---------------------------------------------<div>Teodoro Laino</div><div>Zurich Switzerland</div><div><br></div><div>Contact info:</div><div>Tel.: <a href="http://www.jajah.com/Teo" target="_blank"></a><a href="http://www.jajah.com/Teo" target="_blank"></a><a href="http://www.jajah.com/Teo" target="_blank"><a href="http://www.jajah.com/Teo">http://www.jajah.com/Teo</a></a><span></span></div>
<div><span>E-mail: <a href="mailto:teo...@laino.eu" target="_blank"></a><a href="mailto:teo...@laino.eu" target="_blank"></a><a href="mailto:teo...@laino.eu" target="_blank"><a href="mailto:teo...@laino.eu">teo...@laino.eu</a></a></span></div><div><span> <a href="mailto:teodor...@gmail.com" target="_blank"></a><a href="mailto:teodor...@gmail.com" target="_blank"></a><a href="mailto:teodor...@gmail.com" target="_blank"><a href="mailto:teodor...@gmail.com">teodor...@gmail.com</a></a></span></div>
<font color="#888888"><div>---------------------------------------------</div></font></div><div><div></div><div><div><br>On 10 Jun 2009, at 16:06, Marius Retegan <<a href="mailto:marius.s...@gmail.com" target="_blank"></a><a href="mailto:marius.s...@gmail.com" target="_blank"><a href="mailto:marius.s...@gmail.com">marius.s...@gmail.com</a></a>> wrote:<br>
<br></div><div></div><blockquote type="cite"><div>Hi,<br><br>When using amber parameter files the atomic kind name <br>is automatically generated and is different from the atomic<br>kinds in the amber force field. Is it possible to change this behaviour?<br>
<br>Thanks<br>
Marius<br><br><div class="gmail_quote">On Tue, Jun 9, 2009 at 6:12 PM, Teodoro Laino <span dir="ltr"><<a href="mailto:teodor...@gmail.com" target="_blank"></a><a href="mailto:teodor...@gmail.com" target="_blank"></a><a href="mailto:teodor...@gmail.com" target="_blank"><a href="mailto:teodor...@gmail.com">teodor...@gmail.com</a></a>></span> wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<br>
Regtests are there not to provide meaningful example but for checking<br>
integrity while developing.<br>
In this case that regtest is testing something totally different than<br>
the covalent radius for QMMM.<br>
As you realized by yourself, if you provide the correct types, the right<br>
radius will be parsed and used.<br>
<br>
Teo<br>
<div><br>
<br>
Marius Retegan wrote:<br>
><br>
><br>
> On Tue, Jun 9, 2009 at 5:35 PM, Teodoro Laino <<a href="mailto:teodor...@gmail.com" target="_blank"></a><a href="mailto:teodor...@gmail.com" target="_blank"></a><a href="mailto:teodor...@gmail.com" target="_blank"><a href="mailto:teodor...@gmail.com">teodor...@gmail.com</a></a><br>
</div><div><div></div><div>> <mailto:<a href="mailto:teodor...@gmail.com" target="_blank"></a><a href="mailto:teodor...@gmail.com" target="_blank"></a><a href="mailto:teodor...@gmail.com" target="_blank"><a href="mailto:teodor...@gmail.com">teodor...@gmail.com</a></a>>> wrote:<br>
><br>
><br>
> By default all atoms have the same covalent radius.<br>
><br>
><br>
> I got this.<br>
><br>
><br>
> Please use the tools provided by Axel and the CMM folks<br>
> (covalent_radii.pl, you can get here in this group under Files) if you<br>
> want realistic values.<br>
><br>
><br>
> What confused me is that the input that I was referring to has the<br>
> following section:<br>
> &MM_KIND H<br>
> RADIUS 0.440<br>
> &END MM_KIND<br>
> &MM_KIND O<br>
> RADIUS 0.780<br>
> &END MM_KIND<br>
> With this all atoms get the same radii. So this part of the input it's<br>
> useless.<br>
> If I change it to HT and OT I get the expected values.<br>
> Marius<br>
><br>
><br>
><br>
> Regards<br>
> Teo<br>
><br>
> Marius Retegan wrote:<br>
> > Apparently cp2k assigns the same covalent radius for the MM atoms.<br>
> > I took the input file from tests/QMMM/QS/regtest-4/wat_nacl.inp and<br>
> > changed the print level to medium.<br>
> > This is what I get:<br>
> ><br>
> > MM POINT CHARGES GENERATING THE QM/MM ELECTROSTATIC<br>
> POTENTIAL<br>
> ><br>
> ><br>
> -------------------------------------------------------------------------<br>
> > MM ATOM: 3 RADIUS: 1.511781 CHARGE: 0.417000CORR.<br>
> > RADIUS 1.511781<br>
> > MM ATOM: 4 RADIUS: 1.511781 CHARGE: -0.834000CORR.<br>
> > RADIUS 1.511781<br>
> > MM ATOM: 5 RADIUS: 1.511781 CHARGE: 0.417000CORR.<br>
> > RADIUS 1.511781<br>
> > MM ATOM: 6 RADIUS: 1.511781 CHARGE: 0.417000CORR.<br>
> > RADIUS 1.511781<br>
> > MM ATOM: 7 RADIUS: 1.511781 CHARGE: -0.834000CORR.<br>
> > RADIUS 1.511781<br>
> > MM ATOM: 8 RADIUS: 1.511781 CHARGE: 0.417000CORR.<br>
> > RADIUS 1.511781<br>
> > MM ATOM: 9 RADIUS: 1.511781 CHARGE: 0.417000CORR.<br>
> > RADIUS 1.511781<br>
> > MM ATOM: 10 RADIUS: 1.511781 CHARGE: 1.000000CORR.<br>
> > RADIUS 1.511781<br>
> > MM ATOM: 11 RADIUS: 1.511781 CHARGE: -1.000000CORR.<br>
> > RADIUS 1.511781<br>
> ><br>
> > Atom 3 is an oxygen, while 4 if a hydrogen. Is this related to<br>
> > periodic QM/MM?<br>
> > Thanks<br>
> > Marius<br>
> ><br>
> > ><br>
><br>
><br>
><br>
><br>
><br>
> ><br>
<br>
<br>
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