[gmx-users] g_dist error
Justin A. Lemkul
jalemkul at vt.edu
Tue Sep 13 04:35:28 CEST 2011
aiswarya.pawar at gmail.com wrote:
> Even if I specify an atom say 1277 atom number to find distance against the OW atoms. I get the same result of SOL-OW distance. Is it a bug cause even after specifying one atom from a protein why doesn't it give me the result for the SOL.
As was suggested several messages ago, please do NOT combine -o and -dist. If
you want to measure a distance, use -o. If you want g_dist to print a list of
atoms that satisfy some given criteria, use -dist, but not together.
> Sent from my BlackBerry® on Reliance Mobile, India's No. 1 Network. Go for it!
> -----Original Message-----
> From: "Justin A. Lemkul" <jalemkul at vt.edu>
> Sender: gmx-users-bounces at gromacs.org
> Date: Mon, 12 Sep 2011 07:52:54
> To: Discussion list for GROMACS users<gmx-users at gromacs.org>
> Reply-To: jalemkul at vt.edu,
> Discussion list for GROMACS users <gmx-users at gromacs.org>
> Subject: Re: [gmx-users] g_dist error
> 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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