VMD-L Mailing List
From: jeela keel (jeela22_at_gmail.com)
Date: Mon Jan 23 2012 - 08:09:54 CST
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Hi all , did any body have similar error when using the gofr VMD command, I
dont know what I am doing wrong in the scrip. Thank you for your help.
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"
On Fri, Jan 20, 2012 at 3:43 PM, jeela keel <jeela22_at_gmail.com> wrote:
> 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"
>
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