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?
--
*With regards,*
*Dulal Mondal,*
*Research Scholar,*
*Department of Chemistry,*
*IIT Kharagpur, Kharagpur 721302.*
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Received on Wed May 07 2025 - 01:30:02 PDT
