VMD-L Mailing List

From: jeela keel (jeela22_at_gmail.com)
Date: Fri Jan 20 2012 - 14:43:13 CST

Hi All,

I need to get the cat off of the first hydration shell of a protein, so
using measure gofr to get the rdf between the water and the protein. In
the second selection I chose the water that is in a distance of 4 A from
the protein, and then measured the rdf between the two sections ( also
tried selecting all the water in the system) . However the script give me
following error for 500 frames. I tried many thing like different
selections and different max values but still give same error.
ERROR) measure gofr: bad frame range given. max. allowed frame#: 500
ERROR) measure gofr: bad frame range given. max. allowed frame#: 500
ERROR) measure gofr: bad frame range given. max. allowed frame#: 500
ERROR) measure gofr: unit cell volume is zero.

the script
        setting the number of frames
         set sel1 [atomselect top "protein"]
        #set sel2 [atomselect top "resname SOL "]
        set sel2 [atomselect top "resname SOL and pbwithin 4.00 of protein
"]

        set gr1 [measure gofr $sel1 $sel2 delta .1 rmax 10.0 usepbc 1
selupdate 1 first 1 last $number_frame step 1]
        #set gr1 [measure gofr $sel1 $sel2 delta 0.1 rmax 10.0 usepbc 1
selupdate 1 first 0 last -1 step 1]

        set r [lindex $gr1 0]
        set gr2 [lindex $gr1 1]
        set igr [lindex $gr1 2]
        set i 0
        foreach j $r k $gr2 l $igr {
               puts $outfile1 "$j $k $l"