VMD-L Mailing List

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

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