Hello Vinicius!
Thanks for your quick, and as usual, very helpful reply. Just as a curious follow-up, is there a known scaling relationship for how slowly the predicted pKas converge as a function of the number of titratable groups? Part of the concern behind my question was that having ~80 titratable groups wouldn’t be tractable. If my instinct was wrong on that point, that’s great.
Best,
Matthew
> On Jun 24, 2021, at 2:03 PM, Cruzeiro, Vinicius <vcruzeiro.UCSD.EDU> wrote:
>
> *Message sent from a system outside of UConn.*
>
>
> Hello Matthew,
>
> At the moment, you can control the maximum number of titratable residues inside the source code, at $AMBERHOME/src/pmemd/src/constantph.F90 for pmemd or $AMBERHOME/AmberTools/src/sander/constantph.F90 for Sander. You need to modify the following lines:
>
> ! Limits on the sizes of the data structures
> #define MAX_TITR_RES 50
> #define MAX_TITR_STATES 200
> #define MAX_ATOM_CHRG 1000
> #define MAX_H_COUNT 4
>
> As you can see, the default limit is 50 titratable residues. Once you change the limits above, you need to recompile pmemd and/or sander before running your simulation.
>
> However, we have recently implemented a new namelist in the CPIN file (called CNSTPHE_LIMITS) that specifies these limits. Parmed from AmberTools21 now prints these limits automatically. Sander from AmberTools21 is already capable of reading it, and pmemd from Amber22 will be able as well. Thus, with this change, there is no need any more to recompile the code when you have many titratable residues; from now on, Amber should not complain when users simulate many titratable residues or states, etc 😉
>
> I hope this helps,
> All the best,
>
> Vinícius Wilian D. Cruzeiro, PhD
> Postdoctoral Researcher
> San Diego Supercomputer Center
> Department of Chemistry and Biochemistry
> University of California, San Diego
> Voice: +1(858)246-5584
> Twitter: .vwcruzeiro
> ________________________________
> From: Matthew Guberman-Pfeffer <matthew.guberman-pfeffer.uconn.edu>
> Sent: Thursday, June 24, 2021 9:35 AM
> To: amber.ambermd.org <amber.ambermd.org>
> Subject: [AMBER] Constant pH for large number of titratable residues
>
> Dear Amber Community,
>
> What is the practical limit on the number of residues I should designate as titratable for a constant pH simulation? I want to estimate pKas, as well as study conformational effects at pH extremes (2 versus 10), but my system has 62 acidic and 67 basic residues.
>
> Best regards,
> Matthew
>
>
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Received on Thu Jun 24 2021 - 11:30:02 PDT
