[gmx-users] g_dist error
Justin A. Lemkul
jalemkul at vt.edu
Mon Sep 12 13:52:54 CEST 2011
aiswarya pawar wrote:
> hi Justin,
> As far i referred the OW,HW1 etc are water atoms so how can it be
> distance between the SOL protein atoms, instead it is SOL water atoms.
The printed distance indicates that there is a certain water molecule that is
just over 2 hydrogen bonding lengths away from your protein's backbone. Sounds
normal to me.
> On Mon, Sep 12, 2011 at 4:49 PM, Justin A. Lemkul <jalemkul at vt.edu
> <mailto:jalemkul at vt.edu>> wrote:
> aiswarya pawar wrote:
> Hi Users,
> Am using g_dist to find the distance between water and protein.
> but my output has the values of SOL-water distance.
> t: 1 136 SOL 2336 OW 0.772373 (nm)
> This is not a water-water distance, it is the output of the -dist
> option telling you that water molecule 136 has its OW atom at
> 0.7723273 nm from whatever your reference group is.
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
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Justin A. Lemkul
ICTAS Doctoral Scholar
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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