Re: [AMBER] "mask" command failure

From: Ucisik, Melek Nihan <>
Date: Sun, 9 Aug 2015 20:37:06 +0000

Hello again,
I am not sure if I understand the composition of the output of this command correctly. I am reading in 500 frames and want to get a count of sodiums that are within 2.5 Å of a certain atom (:7.OP1) for each frame. I guess “mask" is not the command I want for that purpose but I still want to understand what it returns exactly. Here are the top few lines from my output:

#Frame AtomNum Atom ResNum Res MolNum
      30 1834 Na+ 93 Na+ 39
      44 1845 Na+ 104 Na+ 50
      44 1913 Na+ 172 Na+ 118
      45 1845 Na+ 104 Na+ 50
      45 1913 Na+ 172 Na+ 118
      46 1845 Na+ 104 Na+ 50
      46 1913 Na+ 172 Na+ 118

So, does this mean:

1. There were no Na+’s within 2.5 Å of :7.OP1 in frames 1-29 and 31-43 etc.
2. In the frame 44, there were 2: residue numbers 104 and 172.
3. In the frame 45, there were 2: residue numbers 104 and 172.
4. In the frame 46, there were 2: residue numbers 104 and 172.

Then what is MolNum?

Also, if I add the “maskpdb” option to the command as shown below (by typing it myself, no copy and paste to eliminate any possible errors as before), it gives a segmentation fault:

mask "(:7.OP1<:2.5)&:Na+" maskout mask_A7OP1_Na.dat maskpdb mask_A7OP1_Na.pdb


----- stripped_prod_ions.netcdf (1-500, 1) -----
 0% Segmentation fault

 Can you help me understand what is going on?



On Aug 7, 2015, at 11:20 AM, Ucisik, Melek Nihan <<>> wrote:

Well, that was exactly what I’ve done: I copied the example in the manual, pasted in my script, and then modified the atom mask without touching the quotes.
I typed the quotes by hand and it worked with no problems.
Thanks, Hai, Dan, and Jason!


On Aug 7, 2015, at 1:21 AM, Jason Swails <<>> wrote:

On Thu, Aug 6, 2015 at 10:51 PM, Daniel Roe <<>> wrote:

Interesting. If I copy the quotes from the email I get that error. If
I input the quotes myself (which is how I originally tested)
everything is fine. Clearly the quotes in the email are a different
character (as further evidenced by the strange character that pops up
in the error message).

​Yes, gmail is all too happy to turn the ASCII quotes into the "fancy"
quotes (note how they don't go straight down, but curl toward the text).
Same type of deal with hyphens getting replaced with n- or m-dashes...
Copy-paste doesn't really work here.

So to Nihan -- make sure you're not copying and pasting from a place that
formats text for humans (like word, email, ... etc.) -- if you're in doubt,
replace your quotes with ones you type by hand (or just get rid of them).

All the best,

Jason M. Swails
Rutgers University
Postdoctoral Researcher
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Received on Sun Aug 09 2015 - 14:00:02 PDT
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