VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Mon Jan 23 2012 - 09:29:37 CST

isn't the error message is self-explanatory?
your argument to the "last" flag is obviously incorrect.

axel.

On Mon, Jan 23, 2012 at 9:09 AM, jeela keel <jeela22_at_gmail.com> wrote:
> 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"
>
> 

-- 
Dr. Axel Kohlmeyer
akohlmey_at_gmail.com  http://goo.gl/1wk0
College of Science and Technology
Temple University, Philadelphia PA, USA.