VMD-L Mailing List

From: Efthymiou, Christos (christos.dereschuk.20_at_ucl.ac.uk)
Date: Tue Aug 30 2022 - 10:09:37 CDT

Hi,

I have a ligand that I would like to prepare simulation files for in QwikMD, but I am having trouble as it contains heteroatoms whose topology+parameters are missing according to QwikMD. I have read through the QwikMD manual, and it says to click the Add Topo+Param button, followed by the selecting the .str file. The ligand is made of sugars, so I have tried selecting the toppar_all36_carb_glycopeptide.str file, but the following error appears when I do this:````
unmatched open quote in list
unmatched open quote in list
while executing
"lindex [lindex $val $i] 0"
(procedure "QWIKMD::addTopParm" line 18)
invoked from within
"QWIKMD::addTopParm"
invoked from within
".qwikmdTopoParam.f1.buttons.add invoke "
invoked from within
".qwikmdTopoParam.f1.buttons.add instate {pressed !disabled} { .qwikmdTopoParam.f1.buttons.add state !pressed; .qwikmdTopoParam.f1.buttons.add invoke }..."
(command bound to event)
````
I can send the PDB file of the ligand, but I would greatly appreciate some help on how I can correctly add the topology and parameter files to be able to simulate the ligand. Do I need to take some additional steps prior to selecting the .str file? How can I fix this error? Thank you!