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?
--Vincent Ustach
University of California, Davis
On Fri, Jul 14, 2017 at 9:34 AM, Vincent Ustach <vustach.ucdavis.edu> wrote:
> 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
>> _______________________________________________
>> AMBER mailing list
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>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>
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Received on Thu Aug 24 2017 - 20:30:02 PDT
