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
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Jul 14 2017 - 02:00:02 PDT
