Hi,
On Fri, Mar 21, 2014 at 8:35 AM, George Tzotzos <gtzotzos.me.com> wrote:
>
> trajin equil_2ns.mdcrd 1 1
> center :1-127 mass origin
> image origin center familiar
> strip_mask = :WAT,Na+,&!:127
> trajout test.pdb pdb
>
'strip_mask' is not a valid ptraj (or cpptraj) command. I think you want:
strip :WAT,Na+,&!:127
See the manual for full details on the 'strip' command.
-Dan
>
> The error message I get is:
>
> PTRAJ: Processing input from file make.in
>
> PTRAJ: trajin equil_2ns.mdcrd 1 1
> Checking coordinates: equil_2ns.mdcrd
> Rank: 0 Atoms: 13282 FrameSize: 322778 TitleSize: 81 NumBox: 3 Seekable 1
>
>
> PTRAJ: center :1-127 mass origin
> Mask [:1-127] represents 2024 atoms
>
> PTRAJ: image origin center familiar
> Mask [*] represents 13282 atoms
>
> PTRAJ: strip_mask = :WAT,Na+,&!:127
>
> ERROR in tokenize(): wrong syntax
> ';
>
> I tried enclosing the expression of the strip_mask in " " and ' ' to no
> avail
>
> Thanks in advance for any suggestions
>
> Regards
>
> George
>
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--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 201
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-6208 (Fax)
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Received on Fri Mar 21 2014 - 08:00:03 PDT
