Hello,
See the file "dynph.h" in $AMBERHOME/src/sander. Alter TITR_RES_C (max
residues) TITR_STATES_C (total number of states across all of your residues)
and ATOM_CHRG_C (total number of partial charges that can be stored for all
of your titratable residues). Don't forget to make clean and recompile
afterwards. Also, make sure that all bug fixes are applied, since there's a
fairly serious bug for parallel constant pH simulations in vanilla amber8,
amber9, and amber10 (I don't think a patch has been made yet for amber8).
Hope this helps,
Jason
On Fri, Aug 20, 2010 at 2:26 PM, <piotrek.vega.umcs.lublin.pl> wrote:
> Dear Amber users,
>
>
> I'm still learing how to use Amber, so sorry if the question is too silly.
>
> I'm running a const-pH calculations on a large protein, and it looks like
> I reached the limit of titratable groups, crash with error:
>
> forrtl: severe (18): too many values for NAMELIST variable, unit 18, file
> /home/d3x582/PIOTR/test_const_ph_even_more_titratable_groups/ph_5/cpin,
> line 40, position 76
>
>
> and lines 40,41 in cpin are:
>
> 'Residue: GL4 341','Residue: AS4 366','Residue: AS4 368','Residue: LYS
> 381',
> 'Residue: AS4 382','Residue: AS4 387','Residue: GL4 391','Residue: GL4
> 394',
>
>
> I am able to run calculations with smaller number of titrable groups (e.g.
> only HIS residues, or HIS,GLU). I did not see any fixed-size arrays in
> constph.f file, the value for the titratable gropus counter (trescnt) is
> set by cpin, so ... how should I modify amber code to increase the number
> of protonatable-residues.
>
> Thank you for help,
> Piotrek
>
>
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> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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Received on Fri Aug 20 2010 - 12:00:04 PDT
