Eric,
I included those changed and recompiled AmberTools. Those modifications
fixed the problem! Thank you very much Jason and Eric for your help.
Sincerely,
Vincent
--Vincent Ustach
University of California, Davis
On Fri, Jul 14, 2017 at 1:48 AM, Eric Lang <eric.lang.bristol.ac.uk> wrote:
> Hi Vincent,
>
>
>
> Have you also modified it in ./AmberTools/src/cphstats/constants.h ?
>
> Personally, I have modified 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
>
> replacing
>
> integer, parameter :: STATEINF_FLD_C = 5
>
> integer, parameter :: TITR_RES_C = 50
>
> integer, parameter :: TITR_STATES_C = 200
>
> integer, parameter :: ATOM_CHRG_C = 1000
>
> with
>
> integer, parameter :: STATEINF_FLD_C = 5
>
> integer, parameter :: TITR_RES_C = 100
>
> integer, parameter :: TITR_STATES_C = 400
>
> integer, parameter :: ATOM_CHRG_C = 2000
>
>
>
> And for pmemd, I modified $AMBERHOME/src/pmemd/src/constantph.F90
>
> Replacing,
>
> #define MAX_TITR_RES 50
>
> #define MAX_TITR_STATES 200
>
> #define MAX_ATOM_CHRG 1000
>
> #define MAX_H_COUNT 4
>
> with
>
> #define MAX_TITR_RES 100
>
> #define MAX_TITR_STATES 400
>
> #define MAX_ATOM_CHRG 2000
>
> #define MAX_H_COUNT 4
>
>
>
> And it seems to work fine. I haven't encountered any problems yet.
>
>
>
> HTH,
>
>
>
> Eric
>
>
>
> ------------------------------
> *From:* Vincent Ustach <vustach.ucdavis.edu>
> *Sent:* 13 July 2017 20:12
> *To:* amber.ambermd.org
> *Subject:* [AMBER] cphstats Error: Could not open or parse cpin file
>
> Dear Jason,
>
> Apologies but I did not have the correct mail settings so I did not see
> your reply until just now in the archive. Since I don't have the email, I
> need to start a new chain. The original messages are at
> http://archive.ambermd.org/201706/0506.html
>
> Per your instructions I modified $AMBERHOME/src/cphstats/parse_cpin.F90 to
>
> #define TITR_RES_C 100
>
> and recompiled the entire suite because I was not sure how to only compile
> cphstats.
>
> Unfortunately now I get a new error:
>
> cphstats -i 4F5S.equil.cpin ph0/4F5S.md1.cpout -o ph0_calckpa.dat
> --population pH0_populations.dat
> Error: Could not open or parse for reading!
> *** stack smashing detected ***: cphstats terminated
> Aborted (core dumped)
>
> It looks like this broke cphstats because it complains even with the HEWL
> tutorial protein that has only 17 residues and gave no problems before the
> recompile:
>
> cphstats -i 4LYT.equil.cpin ph0/4LYT.md1.cpout -o ph0_calcpkaj13.dat
> --population ph0_populationsj13.dat
> Error: Could not open or parse for reading!
> *** stack smashing detected ***: cphstats terminated
> Aborted (core dumped)
>
> I changed the line in $AMBERHOME/src/cphstats/parse_cpin.F90 back to
>
> #define TITR_RES_C 50
>
> and recomplied the entire suite, and HEWL 4LYT can again be analyzed with
> cphstats. FYI this is AmberTools17 (updated from AmberTools16 with
> ./update_amber --upgrade)
>
> Any other suggestions on how to proceed are greatly appreciated.
>
> -Vincent
>
>
> >I believe you have to make a similar change in cphstats. Look for the
> >parse_cpin.F90 file and the TITR_RES_C define at the top. Make the same
> >changes there and recompile cphstats.
> >
> >HTH,
> >Jason
> >
> >On Fri, Jun 30, 2017 at 6:54 PM, Vincent Ustach <vustach.ucdavis.edu>
> wrote:
> >
> >> Hello,
> >>
> >> I have run constant pH MD on bovine serum albumin protein PDB file 4F5S.
> I
> >> feel I should mention that this protein has 80 titratable residues and
> in
> >> order to handle more than 50 residues I have modified the file
> >>
> >> $AMBERHOME/src/sander/dynph.h
> >>
> >> from
> >>
> >> #define TITR_RES_C 50
> >>
> >> to
> >>
> >> #define TITR_RES_C 100
> >>
> >> Now I am experiencing an error with cphstats. Please see below:
> >>
> >> cphstats -i 4F5S.equil.cpin 4F5S.md1.cpout -o pH0_calcpka.dat
> --population
> >> pH0_populations.dat
> >> Error: Could not open or parse 4F5S.md1.cpin for reading!
> >>
> >> See below for the text of 4F5S.equil.cpin, which is unfortunately over
> 500
> >> lines:
>
>
>
> --Vincent Ustach
> University of California, Davis
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Received on Fri Jul 14 2017 - 10:00:03 PDT
