On Thu, Apr 11, 2013 at 2:47 AM, Anselm Horn <
Anselm.Horn.biochem.uni-erlangen.de> wrote:
> Dear Amber developers and users,
>
> we are using the AT12 Fortran program calcpka to analyse constant pH
> simulations (Amber12), but encounter two problems:
>
> First, we noticed that the residue number in the output file
> 'populations.dat' is cut to two digits making it cumbersome to
> identify residues in a protein with more than 99 amino acinds.
>
> Could you please change the output format in line 463 of calcpka.F90
> from '1a15' to at least '1a16'?
>
>
Done. Changed to 1a17, as I can't imagine that anybody will titrate more
than 10K residues :).
Second, when trying to analyze a system with the maximum of 50
> titratable groups with calcpka, we obtain the following error:
>
> At line 203 of file calcpka.F90 (unit = 10, file = 'MD1/ph61d2_prod.cpin')
> Fortran runtime error: Repeat count too large for namelist object resname
>
> Is this an issue of the Gnu gfortran compiler which we used (version
> 4.5.1 20101208)? Is there any workaround?
>
Have you tried changing the parameters in the beginning of calcpka (e.g.
integer, parameter :: STATEINF_FLD_C = 5
integer, parameter :: TITR_RES_C = 50
integer, parameter :: TITR_STATES_C = 200
integer, parameter :: ATOM_CHRG_C = 1000
) to accomodate the large number of residues? Did you make any changes to
dynph.h when you ran the initial constant pH simulations with sander? Any
changes you made there you will have to duplicate in calcpka.F90.
I've personally never even come close to overflowing this allowance, so I
have never seen your errors before...
Good luck,
Jason
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Thu Apr 11 2013 - 08:00:02 PDT
