VMD-L Mailing List

From: Umut Gerlevik (umut.gerlevik_at_gmail.com)
Date: Tue Jul 16 2019 - 05:56:15 CDT

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