Thanks for your suggestion, i did that by extracting the number of water atoms to be removed from prmtop file.
Regards
Steven Winfield <saw44.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.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.
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> >
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Received on Sun Jul 08 2007 - 06:07:39 PDT
