Dear Vinicius
This actually worked. I changed MAX_ATOM_CHRG to 2000 (for sander, in the
dynph.h include file) and the simulation runs fine. Thank you very much.
By the way, I think these max values are so small, you may think of
setting them larger, in the next amber version.
Thanks
Santo
On Fri, 18 Sep 2020 at 18:43, Cruzeiro,Vinicius Wilian D <vwcruzeiro.ufl.edu>
wrote:
> Hello Santo,
>
> All seems fine in your CPIN file. I believe you are having trouble due to
> some limitations inside constantph.F90 that affect the maximum size of the
> arrays in CPIN.
>
> Both at the top of $AMBERHOME/src/pmemd/src/constantph.F90 and of
> $AMBERHOME/AmberTools/src/sander/constantph.F90 you will find the following:
>
> #define MAX_TITR_RES 50
> #define MAX_TITR_STATES 200
> #define MAX_ATOM_CHRG 1000
> #define MAX_H_COUNT 4
>
> MAX_ATOM_CHRG defines the limit of the charge array as 1000, and your CPIN
> has more charges than that (1322, to be exactly). This would explain why
> your CpHMD simulations work when you have less titratable residues, because
> the charge array is smaller, makes sense? Try to change the 4 lines above
> accordingly, recompile whichever MD engine you are using (sander or pmemd),
> and I expect your problem to be solved.
>
> I hope this helps,
> And please let me know if you need any assistance further,
>
>
> Vinícius Wilian D. Cruzeiro
>
> PhD Candidate
> Department of Chemistry, Physical Chemistry Division
> University of Florida, United States
>
> Voice: +1(352)846-1633
>
> ________________________________
> From: Kolattukudy P. Santo <santotheophys.gmail.com>
> Sent: Thursday, September 17, 2020 1:34 PM
> To: AMBER Mailing List <amber.ambermd.org>
> Subject: Re: [AMBER] constant pH error
>
> [External Email]
>
> Dear Vinicius
> Thanks for the reply. I attach the cpin file, which for a 20 segment
> chain.
>
> Santo
>
>
> On Thu, 17 Sep 2020 at 11:06, Cruzeiro,Vinicius Wilian D <
> vwcruzeiro.ufl.edu>
> wrote:
>
> > Hello Santo,
> >
> > Could you show your CPIN file that is failing?
> >
> > Thanks,
> >
> >
> > Vinícius Wilian D Cruzeiro
> >
> > PhD Candidate
> > Department of Chemistry, Physical Chemistry Division
> > University of Florida, United States
> >
> > Voice: +1(352)846-1633<tel:+1(352)846-1633>
> >
> > On Sep 16, 2020, at 8:18 PM, Kolattukudy P. Santo <
> santotheophys.gmail.com>
> > wrote:
> >
> > [External Email]
> >
> > Hello all
> > I defined and parameterized some new titratable residues in
> > explicit solvent for the cpHMD run. They running fine, but some
> combination
> > of them ( into oligomers ) giving me error
> > --
> > At line 167 of file constantph.F90 (unit = 23, file = 'jbl2.cpin')
> > Fortran runtime error: Cannot match namelist object name 0.083403
> > --
> > If A ,B,C are the residues, then A-B-C gives error, while A-B, B-C etc
> > work fine.
> > This is a strange error that I could not understand. Please advise, how
> to
> > resolve this.
> >
> > Thanks a lot
> > Santo
> >
> >
> >
> > --
> > Best,
> > KP Santo
> > --------------------------------------------------------------
> > Dr. Kolattukudy P. Santo
> > Post doctoral Associate
> > Department of Chemical and Biochemical Engineering
> > Rutgers, The State University of New Jersey
> > New Brunswick, New jersey
> > USA
> > ---------------------------------------------------------
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> >
> >
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>
> --
> Best,
> KP Santo
> --------------------------------------------------------------
> Dr. Kolattukudy P. Santo
> Post doctoral Associate
> Department of Chemical and Biochemical Engineering
> Rutgers, The State University of New Jersey
> New Brunswick, New jersey
> USA
> ---------------------------------------------------------
> _______________________________________________
> AMBER mailing list
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> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Best,
KP Santo
--------------------------------------------------------------
Dr. Kolattukudy P. Santo
Post doctoral Associate
Department of Chemical and Biochemical Engineering
Rutgers, The State University of New Jersey
New Brunswick, New jersey
USA
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Received on Sat Sep 19 2020 - 20:30:02 PDT
