Date: Mon Aug 28 2006 - 06:50:33 CDT


I want to identify the water molecules within 2 angstroms of certain residues
for each frame of a trajectory. I am using the following script:

set sel [atomselect top "name O and resname WAT and within 2 of residue 0"]
set n [molinfo top get numframes]
for { set i 0 } { $i < $n } { incr i } {
$sel frame $i
$sel update
$sel writepdb water_$i.pdb

However I am having problems with the numbering of the waters. For instance, for
residue 0 and frame 0 I obtain one water molecule with the number X1546.
However, If I apply the same script only to the pdb file corresponding to the
frame 0, the same water molecule is now numbered 910, which is correct. It
seems that the water molecules in the trajectory are being wrongly numbered...

What am I doing wrong? Is there any other simple way to do this type of
analysis? My trajectory is from amber.

Thanks in advance

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