I've been trying to run MMPBSA calculations using CAFE, however, when I use -pb_rad charmm. VMD prints the following error when it begins to run PB calculations:"Unmatched open quote in list "
I suspect that the error originates from the following section of the cafe_mmpsa script:
if { $pb } { show -info "Calculating the PB term" set start [clock seconds] # assign radii set ar_args "$currmol $pb_rad" if { $pb_rad eq "charmm" } { foreach p $parfile { append ar_args " \"$p\"" } } elseif { $pb_rad eq "parm7" } { append ar_args " \"$topfile\"" } eval assign_radii $ar_args set com_pb_list [calc_pb $currmol com $comsel] if { $recsel ne "" } { set rec_pb_list [calc_pb $currmol rec $recsel] } if { $ligsel ne "" } { set lig_pb_list [calc_pb $currmol lig $ligsel] } foreach { d h m s } [timer $start] { break } show -info "It took $d days $h hrs $m min $s sec"}However I need help identifying the part that needs correction. I am hoping someone can help me or recommend any other PB Radius I could use.
Thank you, Javier
