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 Thu Jul 13 2017 - 12:30:03 PDT
