AMBER Archive (2008)

Subject: Re: AMBER: ptraj selection

From: Ilyas Yildirim (yildirim_at_pas.rochester.edu)
Date: Thu Jul 10 2008 - 19:58:08 CDT

Dear Jianyin,

I have attached 3 files: prmtop.nowater, ptraj_heavy.in and
gacc_A-form.pdb. I want to mask the atoms of
"(:1-4_at_C1',C2',C3',C4',C5',O4',O5',O3',P) | (:1,2_at_N9,C8,C4) |
(:3,4_at_N1,C2,C6)" in ptraj input file, but I am not sure if I can do that.
Thanks in advance for your help.

Best,

On Thu, 10 Jul 2008, Jianyin Shao wrote:

> Hi, Ilyas,
>
> Would you mind sending me your prmtop file and crd file so I can take a
> look. Ptraj uses a separate routine, other than the ambmask, to parse atom
> masks. However, we try to match the specification described in the ambmask
> manual.
>
> Thanks,
>
> Jianyin
> 

-- 
  Ilyas Yildirim
  ---------------------------------------------------------------
  = Department of Physics        -                              =
  = University of Rochester      -                              =
  = 585-275-6766 (office)        - 585-267-5644 (home)          =
  = http://www.pas.rochester.edu/~yildirim/                     =
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