Re: [AMBER] "mask" command failure

From: Ucisik, Melek Nihan <>
Date: Tue, 11 Aug 2015 15:20:38 +0000

Still 14.09 actually.


On Aug 10, 2015, at 12:16 PM, Daniel Roe <<>> wrote:

On Sun, Aug 9, 2015 at 2:37 PM, Ucisik, Melek Nihan <<>> wrote:
#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.

Yes to all.

Then what is MolNum?

Molecule number (current documentation needs to be updated, thanks for
pointing this out!).

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:

Are you still using version 14.09 or have you upgraded to 15?


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
AMBER mailing list<><>

AMBER mailing list<><>

AMBER mailing list<>

Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 307
Salt Lake City, UT 84112-5820
(801) 587-9652
(801) 585-6208 (Fax)

AMBER mailing list<>

AMBER mailing list
Received on Tue Aug 11 2015 - 08:30:04 PDT
Custom Search