AMBER Archive (2007)

Subject: Re: AMBER: Stirp command in ptraj

From: Carlos Simmerling (carlos.simmerling_at_gmail.com)
Date: Fri Jul 06 2007 - 11:45:43 CDT

yes it will

On 7/6/07, priya priya <priyaanand_27_at_yahoo.co.in> wrote:
> Thanks it works!
> i want to create pdb file from nowater.mdcrd file,Will ptraj do that?
> Regards
>
>
> Steven Winfield <saw44_at_cam.ac.uk> wrote:
> Try removing the space before WAT
>
> >strip : WAT
> ^
>
> Steve
>
> priya priya wrote:
> > hi,
> > i am writing all the input commands i am doing:
> >>ptraj am15_wat.prmtop <
> >>trajin am15_rem.mdcrd
> >>strip : WAT
> >>trajout am15_nwat.mdcrd
> > EOF
> >
> > it gave segmantation fault.
> >
> > Now i calculated the no of indices of water molecules from the prmtop
> > file and did it another way like
> > >ptraj am15_wat.prmtop <
> >>trajin am15_rem.mdcrd
> >>strip : 423-98707
> >>trajout am15_nwat.mdcrd
> > EOF
> >
> > the command is working results :
> >
> > PTRAJ: Processing input from "STDIN" ...
> >
> > PTRAJ: trajin am15_rem.mdcrd.rep1
> > Checking coordinates: am15_rem.mdcrd.rep1
> >
> > PTRAJ: strip :423-98708
> > Mask [:423-98708] represents 97110 atoms
> >
> > PTRAJ: trajout am15_rem_nwat.mdcrd
> >
> > PTRAJ: Successfully read the input file.
> > Coordinate processing will occur on 800 frames.
> > Summary of I/O and actions follows:
> >
> > INPUT COORDINATE FILES
> > File (am15_rem.mdcrd.rep1) is an AMBER trajectory (with box info) with
> > 800 sets
> >
> > OUTPUT COORDINATE FILE
> > File (am15_rem_nwat.mdcrd) is an AMBER trajectory (with box info)
> >
> > ACTIONS
> > 1> STRIP: 97110 atoms will be removed from trajectory: :423-32792
> >
> >
> > Processing AMBER trajectory file am15_rem.mdcrd.rep1
> >
> > Set 1 .................................................
> > Set 50 .................................................
> > Set 100 .................................................
> > Set 150 .................................................
> > Set 200 .................................................
> > Set 250 .................................................
> > Set 300 .................................................
> > Set 350 .................................................
> > Set 400 .................................................
> > Set 450 .................................................
> > Set 500 .................................................
> > Set 550 .................................................
> > Set 600 .................................................
> > Set 650 .................................................
> > Set 700 .................................................
> > Set 750 .................................................
> > Set 800
> >
> > PTRAJ: Successfully read in 800 sets and processed 800 sets.
> > Dumping accumulated results (if any)
> >
> > Regards
> >
> >
> > */Carlos Simmerling /* wrote:
> >
> > people have a tendency to do this, where they give us what they
> > think they
> > are using and not the actual input. This can waste our time if you
> > introduce a typo or
> > extra spaces, etc. If you want help, show us EXACTLY what you used as
> > input and what you got for an error message. Don't re-type it, copy
> > and paste it.
> >
> >
> > On 7/6/07, *priya priya* < priyaanand_27_at_yahoo.co.in
> > > wrote:
> >
> > i am using the file name in the command it is just a symbol in
> > my mail to ask
> >
> >
> > */Steven Winfield >/*
> > wrote:
> >
> > Dear Priya
> >
> > Try specifying the actual file names instead of *'s
> >
> > Steve
> >
> > priya priya wrote:
> > > Dear All,
> > >
> > > I am trying to strip the water molecules from the mdcrd
> > files using
> > > ptraj commans
> > >>trajin *.mdcrd
> > >>strip : WAT
> > >>trajout **.mdcrd
> > >
> > > But it gives error segmentation error and no other details
> > of the
> > > job.Please suggest the error.
> > > Regards
> > >
> > > Send free SMS to your Friends on Mobile from your Yahoo!
> > Messenger.
> > > Download Now! http://messenger.yahoo.com/download.php
> > >
> >
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