On Thu, Aug 24, 2017 at 11:22 PM, Vincent Ustach <vustach.ucdavis.edu>
wrote:
> Hi all,
>
> I complied ambertools again by modifying the following files
>
> ./AmberTools/src/etc/calcpka.F90
> ./AmberTools/src/pbsa/dynph.h
> ./AmberTools/src/cphstats/constants.h
> ./AmberTools/src/cphstats/parse_cpin.F90
> ./AmberTools/src/gbnsr6/dynph.h
> ./AmberTools/src/sander/dynph.h
>
>
> with the following definitions
>
> #define MAX_TITR_RES 200
> #define MAX_TITR_STATES 800
> #define MAX_ATOM_CHRG 4000
> #define MAX_H_COUNT 4
>
> I simulated 4F5S, with 195 titratable residues, and 4LYT, with 18 residues.
> The constant pH MD works fine, but I can not analyze these files with
> cphstats. I get an error I have seen before:
>
> vdustach$ cphstats -i 4F5S.equil.cpin 4F5S.md1.cpout -o calcpka_0.dat
> --population pop_0.dat
> Error: Could not open or parse 4F5S.equil.cpin for reading!
>
> I get this error for 4F5S and 4LYT.
>
> In the current configuration, I am still able to analyze my old files,
> which were created from simulations when the default values were in place:
>
> #define MAX_TITR_RES 50
> #define MAX_TITR_STATES 200
> #define MAX_ATOM_CHRG 1000
> #define MAX_H_COUNT 4
>
> as well as the first change I made
>
> #define MAX_TITR_RES 100
> #define MAX_TITR_STATES 400
> #define MAX_ATOM_CHRG 2000
> #define MAX_H_COUNT 4
>
> Is there an inherent problem with this many possible titratable residues?
>
You need to have the same values in parse_cpin.F90 and constants.h in the
cphstats code. If they are different, stack smashing and chaos ensue. I'm
not quite sure what I was thinking when I duplicated all those constants in
two files; there's no need for it.
I've adjusted the code so that in the future you will only need to modify
constants.h. That said, if you make those changes in both files
(parse_cpin.F90 and constants.h), cphstats should work fine with more than
100 residues.
Good luck,
Jason
--
Jason M. Swails
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Aug 28 2017 - 19:00:03 PDT
