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<div>Hi,</div>
<div>thank you very much! That makes perfectly sense, even though I still don't really know what to do. :D </div>
<div>I guess I have to exclude the CMAP interactions. Or would you suggest using another force field? I want to simulate ATPase function of a Protein. </div>
<div>Best regards,</div>
<div>Nicor </div>
<div>
<div name="quote" style="margin:10px 5px 5px 10px; padding: 10px 0 10px 10px; border-left:2px solid #C3D9E5; word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;">
<div style="margin:0 0 10px 0;"><b>Gesendet:</b> Donnerstag, 10. März 2016 um 15:59 Uhr<br/>
<b>Von:</b> "Groenhof, Gerrit" <ggroenh@gwdg.de><br/>
<b>An:</b> "gromacs.org_gmx-users@maillist.sys.kth.se" <gromacs.org_gmx-users@maillist.sys.kth.se><br/>
<b>Betreff:</b> Re: [gmx-users] QM/MM error: no such bonded interactions with 5 atoms (Mark Abraham)</div>
<div name="quoted-content">Hi,<br/>
<br/>
The problem is that the QM/MM code checks all bonded interactions until 4 atoms, which at the time it was implemented, was the maximum, i.e. before CMAP.<br/>
<br/>
However, I am not sure whether the CMAP interactions should be in or excluded. Excluding will alter the backbone energetics in your QM/Charmm calculations, while including could lead to spurious interactions.<br/>
<br/>
In both cases, in gmxpreprocess/topio.c one needs to add a case 5 to the switch(nratoms) in the generate_qmexcl_moltype in which one either keeps this interaction, or removes it.<br/>
<br/>
best,<br/>
<br/>
Gerrit<br/>
<br/>
Hi,<br/>
<br/>
CHARMM27 uses CMAP dihedrals that have 5 atoms. How that relates to your<br/>
topology isn't clear on the information you've provided. In what context<br/>
did you get the error message?<br/>
<br/>
Mark<br/>
<br/>
On Thu, Mar 10, 2016 at 12:58 PM Roman Zeiss <romanzeiss@gmx.net> wrote:<br/>
<br/>
> Dear Gromacs users,<br/>
><br/>
> I am trying to set up a QM/MM simulation on Gromacs 5.0.4 with Charmm27. I<br/>
> get the error "no such bonded interactions with 5 atoms" when I try to run<br/>
> the simulation. What I did so far:<br/>
><br/>
> 1. I modified the force field files atomtypes.atp and ffnonbonded.itp to<br/>
> include the atom type "LA" and also added a residue file "la.rtp".<br/>
><br/>
> 2. In my topology file for the Protein I have (after adding the LA atoms<br/>
> to that chain at position 1763 and 1764):<br/>
> [ virtual_sites2 ]<br/>
> ; LA QMatom MMatom func length<br/>
> 1763 30 32 1 0.65<br/>
> 1764 1747 1745 1 0.65<br/>
> [ constraints ]<br/>
> ; QMatom MMatom func length<br/>
> 30 32 2 0.153<br/>
> 1747 1745 2 0.153<br/>
><br/>
> 3. Then I created an index.ndx with a group [ QMatoms ].<br/>
><br/>
> 4. For all bonds between QMatoms I changed the bond type from 1 to 5.<br/>
><br/>
> Do I have to change anything more like dihedrals or something? Maybe<br/>
> delete bonds/dihedrals containing the connecting atoms? But nothing so far<br/>
> changed the error message.<br/>
><br/>
> I appreciate any kind of advice very much!<br/>
> Thanky you and best regards,<br/>
> Roman<br/>
><br/>
><br/>
><br/>
><br/>
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