Hi,
Not sure about what's going on exactly, but you might want to try:
1) Upgrading to a more recent version of AmberTools.
2) Using the '--mask' command line flag of cpptraj. The mask parser in
cpptraj may be a bit more robust. E.g.
cpptraj -p CPLX_Neut_Sol.prmtop --mask
":2329-2330,2364,2374,2452,2464,2505,2597,2689,2721,2748-2749,2796,2818,2885&.CA="
Since you're not doing a distance-based mask you shouldn't need the coordinates.
-Dan
On Fri, Mar 20, 2020 at 5:36 AM Oliver Grant <olivercgrant.gmail.com> wrote:
>
> 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 Wed Mar 25 2020 - 13:00:02 PDT
