Hi,
I'm no expert in constant pH simulations, but I read in the Amber25
manual on page 592:
"Note that there is currently no support for titrating N or C terminal
residues."
This should explain the outcome of your cpinutil.py run.
Hope that helps.
Anselm
Bioinformatik | NHR.FAU
Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU)
Germany
Am 07.05.2025 um 10:00 schrieb Dulal Mondal via AMBER:
> Dear Experts,
>
> I am trying to titrate the end terminal residue using constant pH molecular
> dynamics simulation.
>
> But When I type the following command.
> cpinutil.py -o amber18.cpin -op amber18.prmtop -p AMBER.prmtop -igb 2
> -resnames AS4 GL4 HIP TYR LYS.
>
> I also paste the amber18.cpin file.
>
> PROTCNT=2,1,1,1,0,0,1,1,1,1,0,1,1,1,1,
> RESNAME='System: Unknown','Residue: HIP 2','Residue: TYR 5','Residue: HIP
> 8',
> 'Residue: GL4 12','Residue: HIP 13','Residue: HIP 15','Residue: AS4 17',
> 'Residue: GL4 24','Residue: AS4 30','Residue: AS4 32','Residue: HIP 34',
> 'Residue: TYR 38','Residue: AS4 39','Residue: TYR 49','Residue: AS4 50',
> 'Residue: HIP 62','Residue: GL4 67','Residue: AS4 69','Residue: AS4 70',
> 'Residue: AS4 73','Residue: AS4 83','Residue: TYR 86','Residue: AS4 99',
> 'Residue: GL4 104','Residue: HIP 105','Residue: AS4 108','Residue: TYR
> 112',
> 'Residue: GL4 115','Residue: HIP 120','Residue: TYR 125','Residue: AS4
> 127',
> 'Residue: AS4 136','Residue: AS4 159','Residue: AS4 162','Residue: AS4
> 172',
> 'Residue: AS4 177','Residue: GL4 184','Residue: AS4 187','Residue: TYR
> 188',
> 'Residue: TYR 191','Residue: GL4 202','Residue: GL4 211','Residue: GL4
> 218',
> 'Residue: GL4 231','Residue: GL4 233','Residue: GL4 235','Residue: GL4
> 236',
> 'Residue: AS4 240',
> RESSTATE=0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,
> 0,0,0,0,0,0,0,0,0,0,0,0,0,
>
> It does not include the 1st residue. In my system the first residue is his.
> so I it include as titratable residue?
>
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Received on Tue May 13 2025 - 03:30:02 PDT
