Hi Manish,
I had recenly also similar problem... So however I am not sure if this
might
help in your case, before you obtain some better/(more qualified) advices
try just this simple experiment.
Before any actions (reimaging, closestwaters) try first to convert
relevant DCD
trajectory (or it's part) into amber MDCRD format. Then use this
reformated MDCRD
trajectory for any other actions.
Best wishes,
Marek
Dne Thu, 19 May 2011 19:01:34 +0200 Manish <manish.datt.hotmail.com>
napsal/-a:
> Hi All,
>
>
> I'm trying to calculate closest water around protein in a NAMD dcd
> trajectory using ptraj. But I'm getting some water molecules that are not
> near protein (see attached image). I guess this is an issue related to
> imaging.
>
> I'm using following ptraj command:
>
> center :1-105 mass origin
>
> image origin center
>
>
> Kindly let me know what I am doing wrong here.
>
>
> Regards,
>
>
> Manish
>
>
>
>
>
> __________ Informace od ESET NOD32 Antivirus, verze databaze 6135
> (20110519) __________
>
> Tuto zpravu proveril ESET NOD32 Antivirus.
>
> http://www.eset.cz
>
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Received on Thu May 19 2011 - 11:00:03 PDT
