AMBER Archive (2007)

Subject: Re: AMBER: Stirp command in ptraj

From: priya priya (priyaanand_27_at_yahoo.co.in)
Date: Fri Jul 06 2007 - 08:27:27 CDT

hi,
i am writing all the input commands i am doing:
>ptraj am15_wat.prmtop <<EOF
>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 <<EOF
>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 <carlos.simmerling_at_gmail.com> 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 <saw44_at_cam.ac.uk> 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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