VMD-L Mailing List
From: Javier Ivan Wong Romero (jwong_at_cicese.edu.mx)
Date: Thu Oct 07 2021 - 20:38:11 CDT
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Hello
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
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