Hi all,
I'm experiencing an odd error with ambmask:
$ ambmask -p CPLX_Neut_Sol.prmtop -c CPLX_Neut_Sol.rst7 -out amber -find
":2329-2330,2364,2374,2452,2464,2505,2597,2689,2721,2748-2749,2796,2818,2885
& .CA="
| New format PARM file being parsed.
| Version = 1.000 Date = 03/19/20 Time = 05:57:07
natom = 302011
nres = 83801
original : ====
tokenized: ====
postfix : ==;==
Error in group input::atommask.f::pop_evalstack
stack underflow
However if I remove the first residue number (2329) it works fine:
$ ambmask -p CPLX_Neut_Sol.prmtop -c CPLX_Neut_Sol.rst7 -out amber -find
":2330,2364,2374,2452,2464,2505,2597,2689,2721,2748-2749,2796,2818,2885 &
.CA="
| New format PARM file being parsed.
| Version = 1.000 Date = 03/19/20 Time = 05:57:07
natom = 302011
nres = 83801
original :
==:2330,2364,2374,2452,2464,2505,2597,2689,2721,2748-2749,2796,2818,2885 &
.CA=;==
tokenized:
==[:2330,2364,2374,2452,2464,2505,2597,2689,2721,2748-2749,2796,2818,2885]&[.CA=];==
postfix :
==[:2330,2364,2374,2452,2464,2505,2597,2689,2721,2748-2749,2796,2818,2885][.CA=]&;==
14 atoms selected
ATOM 36015 36015
ATOM 36526 36526
ATOM 36678 36678
ATOM 37916 37916
ATOM 38092 38092
ATOM 38704 38704
ATOM 40165 40165
ATOM 41525 41525
ATOM 41994 41994
ATOM 42367 42367
ATOM 42384 42384
ATOM 43063 43063
ATOM 43381 43381
ATOM 44478 44478
If I delete the last (not shown) or second last residue number it also
works:
$ ambmask -p CPLX_Neut_Sol.prmtop -c CPLX_Neut_Sol.rst7 -out amber -find
":2329-2330,2364,2374,2452,2464,2505,2597,2689,2721,2748-2749,2796,2818 &
.CA="
| New format PARM file being parsed.
| Version = 1.000 Date = 03/19/20 Time = 05:57:07
natom = 302011
nres = 83801
original :
==:2329-2330,2364,2374,2452,2464,2505,2597,2689,2721,2748-2749,2796,2818 &
.CA=;==
tokenized:
==[:2329-2330,2364,2374,2452,2464,2505,2597,2689,2721,2748-2749,2796,2818]&[.CA=];==
postfix :
==[:2329-2330,2364,2374,2452,2464,2505,2597,2689,2721,2748-2749,2796,2818][.CA=]&;==
14 atoms selected
ATOM 36001 36001
ATOM 36015 36015
ATOM 36526 36526
ATOM 36678 36678
ATOM 37916 37916
ATOM 38092 38092
ATOM 38704 38704
ATOM 40165 40165
ATOM 41525 41525
ATOM 41994 41994
ATOM 42367 42367
ATOM 42384 42384
ATOM 43063 43063
ATOM 43381 43381
It looks from a few tests that I can remove any one of the above residues
from the selection and it will work. An entirely different set of residues
also has this behaviour, once I get above a certain number of them I get
the stack underflow.
This is Amber14 and Ambertools 14. Let me know if there's any more info I
can send. The prmtop and rst7 are 62Mb and 11Mb. How would I best share
these with the mailing list?
Best,
Oliver
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Received on Fri Mar 20 2020 - 03:00:02 PDT
