Hi,
if you happened to run NVE or NVT simulations you can use the "box" command
in ptraj to set the right cell parameters.
george
2011/5/19 Marek Maly <marek.maly.ujep.cz>
> 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
> >
>
>
> --
> Tato zpráva byla vytvořena převratným poštovním klientem Opery:
> http://www.opera.com/mail/
>
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Received on Thu May 19 2011 - 11:00:04 PDT
