VMD-L Mailing List

From: Joao Ribeiro (jribeiro_at_ks.uiuc.edu)
Date: Tue Jul 16 2019 - 09:29:31 CDT

Dear Umut,

 

Although the “Generate Missing QM Region Topology” lets the user create a fake topology for molecules that have no topology, QwikMD still relies on the elements that are supported by the CHARMM forcefield, which are H, Fe, C, N, O, S, P, He, Ne, Li, Na, Mg, K, Ca, Rb, Cs, Ba, Zn, Cd, Cl, Br, I, F, Al, for the cases the user intends to run a classical equilibration simulation before running the QM/MM simulation. During the classical simulation, the QM region and the solute 5A around are kept frozen so the solvent can equilibrate around it.

 

For now, If you are NOT running the classical simulation, I would suggest you generate the stream file for these two elements based on the other elements present in the “toppar_water_ions.str” and feed this topology to the QwikMD. Please be aware that these topologies and parameters should not be used to run classical (production) simulations. In the QM/MM simulations, the CHARMM parameters of the QM region are ignored. 

 

I hope this helps

 

Best

 

João

 

From: <owner-vmd-l_at_ks.uiuc.edu> on behalf of Umut Gerlevik <umut.gerlevik_at_gmail.com>
Date: Tuesday, July 16, 2019 at 5:57 AM
To: <vmd-l_at_ks.uiuc.edu>
Subject: vmd-l: Generate QM Region Topology in QwikMD for metal ions to perform QM/MM

 

Hi,

 

I want to perform QM/MM simulations for protein systems including Cu(2+) or Hg(2+) in QM region, but I have a problem in "Generate Missing QM Region Topology" of QwikMD. The process is as below:

 

- Open QwikMD Advanced Run tab.

- Browse and load the pdb file containing protein and one Cu(2+) ion.

- In Structure Manipulation/Check, one error in Topologies & Parameters, which is Cu ion.

- Select Cu and open Add Topo+Param, then open Generate QM Region Topology.

- In Generate Toplogy region, select the residue and then write total charge as 2.00. Also there is a file name Cu.rtf.

- Click Generate Topology button and I got the error message below:

 

---Begin---

Application Error

Error:

can't read "QWIKMD::element(Cu)": no such element in array
can't read "QWIKMD::element(Cu)": no such element in array
    while executing
"set atomtype $QWIKMD::element($element)"
    (procedure "QWIKMD::generateTopology" line 24)
    invoked from within
"QWIKMD::generateTopology"
    invoked from within
".qwikmdeditAtm.f1.frameInfo.topoframe.genTop.btt invoke "
    invoked from within
".qwikmdeditAtm.f1.frameInfo.topoframe.genTop.btt instate {pressed !disabled} { .qwikmdeditAtm.f1.frameInfo.topoframe.genTop.btt state !pressed; .qwikm."
    (command bound to event)

---End---

 

I couldn't find any information to solve this issue. I will be appriciated if you can help. Thanks in advance.

 

Umut Gerlevik