Hello Jacopo,
Is there any specific reason why you are titrating such a large number of residues (115)? For example, in general, the pKas of AS4 and LYS differ by a few pH units. Thus, it is unlikely you will get all your AS4 and LYS to titrate at the same time at a given pH value.
If you change the following line at $AMBERHOME/amber/src/pmemd/src/constantph.F90 and recompile pmemd, the calculation will probably work (as it worked in sander with the equivalent modification, as you said).
#define MAX_TITR_RES 50
However, titrating more residues decreases the computational performance of your calculation. People generally titrate only the residues of interest for a given value of pH (or pH range), or the residues of interest for a given study, instead of titrating all possible residues. Before you run your production simulation, you may also perform a short simulation titrating all just to check which residues are important to you.
I hope this helps,
Best,
Vinícius Wilian D Cruzeiro
PhD Candidate
Department of Chemistry, Physical Chemistry Division
University of Florida, United States
Voice: +1(352)846-1633
________________________________
From: Jacopo Sgrignani <sgrigna.gmail.com>
Sent: Thursday, March 8, 2018 10:50:53 AM
To: AMBER Mailing List
Subject: Re: [AMBER] constant pH simulations pemed.cuda
Dear Vinicius
here the file.
thanks
jacopo
2018-03-08 16:48 GMT+01:00 Cruzeiro,Vinicius Wilian D <vwcruzeiro.ufl.edu>:
> Hello Jacopo,
>
>
> Could you please copy here your ph.cpin file?
>
>
> Regards,
>
>
> Vinícius Wilian D Cruzeiro
>
> PhD Candidate
> Department of Chemistry, Physical Chemistry Division
> University of Florida, United States
>
> Voice: +1(352)846-1633
>
> ________________________________
> From: Jacopo Sgrignani <sgrigna.gmail.com>
> Sent: Thursday, March 8, 2018 10:45:53 AM
> To: AMBER Mailing List
> Subject: [AMBER] constant pH simulations pemed.cuda
>
> Dear all
>
> I'm trying to run constant pH simulation with pmemd.cuda in Amber16 but I
> get
>
> this error:
>
> At line 164 of file constantph.F90 (unit = 23, file = 'ph.cpin')
>
> Fortran runtime error: Cannot match namelist object name 'residue:
>
>
>
> Reading other messages I understood that is due to a limit on the number of
> aminoacids that
>
> can be titrated.
>
>
> Changing the limit in the dynph.h I was able to run the calculation with
> sander but not with pmemd.cuda.
>
>
> Could you give me some advice?
>
>
> thanks
>
>
> Jacopo
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Received on Thu Mar 08 2018 - 08:30:02 PST
