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">teodor...@gmail.com</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">http://www.jajah.com/Teo</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">teo...@laino.eu</a></span></div><div><span> <a href="mailto:teodor...@gmail.com" target="_blank"></a><a href="mailto:teodor...@gmail.com" target="_blank">teodor...@gmail.com</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">marius.s...@gmail.com</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">teodor...@gmail.com</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">http://www.jajah.com/Teo</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">teo...@laino.eu</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">teodor...@gmail.com</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">marius.s...@gmail.com</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">teodor...@gmail.com</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">teodor...@gmail.com</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">teodor...@gmail.com</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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