Members of AmberMD,
I am attempting a pH-dependent REMD on a model of RNA I created. The bases
I will be titrating are cytidines. CP is available as a titratable residue
in titratable_residues.py, so we will use that. However, it does not appear
that radius of N3 vs N3-H3+ gets changed in the constant-pH MD. This might
inhibit the close approach of a protonated and unprotonated C:CP base pair.
For ASP and GLU, the script cpinutil.py adjusts the radius of the
unprotonated forms, but the script is limited to carboxylic acids. Should
we try to modify cpinutil.py so that it will also alter the radius of
unprotonated CP? Alternatively, is it possible to add a segment to the cpin
file which will change the ionic radii? I have added my cpin file below.
&CNSTPH
CHRGDAT=1.1662,-0.776,-0.776,-0.4989,0.0558,0.0679,0.0679,0.1065,0.1174,
-0.3548,0.0066,0.2029,-0.0484,0.0053,0.1958,-0.5215,0.1928,0.8185,-0.953,
0.4234,0.4234,-0.7584,0.7538,-0.6252,0.2022,0.0615,0.067,0.
0972,-0.6139,0.4186,
-0.5246,0.0,1.1662,-0.776,-0.776,-0.4989,0.0558,0.0679,0.
0679,0.1065,0.1174,
-0.3548,0.0066,0.2029,0.1954,0.0028,0.2366,-0.4218,0.2253,0.6466,-0.8363,
0.4518,0.4518,-0.4871,0.5039,-0.4753,0.2022,0.0615,0.067,0.
0972,-0.6139,0.4186,
-0.5246,0.4128,
PROTCNT=1,2,
RESNAME='System: Unknown','Residue: CP 5','Residue: CP 7','Residue: CP 18',
'Residue: CP 21',
RESSTATE=0,1,0,0,
STATEINF(0)%FIRST_ATOM=131, STATEINF(0)%FIRST_CHARGE=0,
STATEINF(0)%FIRST_STATE=0, STATEINF(0)%NUM_ATOMS=32,
STATEINF(0)%NUM_STATES=2,
STATEINF(1)%FIRST_ATOM=197, STATEINF(1)%FIRST_CHARGE=0,
STATEINF(1)%FIRST_STATE=0, STATEINF(1)%NUM_ATOMS=32,
STATEINF(1)%NUM_STATES=2,
STATEINF(2)%FIRST_ATOM=558, STATEINF(2)%FIRST_CHARGE=0,
STATEINF(2)%FIRST_STATE=0, STATEINF(2)%NUM_ATOMS=32,
STATEINF(2)%NUM_STATES=2,
STATEINF(3)%FIRST_ATOM=656, STATEINF(3)%FIRST_CHARGE=0,
STATEINF(3)%FIRST_STATE=0, STATEINF(3)%NUM_ATOMS=32,
STATEINF(3)%NUM_STATES=2,
STATENE=0.000000,43.152046,
TRESCNT=4,CPHFIRST_SOL=754, CPH_IGB=2, CPH_INTDIEL=1.0,
/
Thank You,
Paul Freidhoff
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Received on Mon Oct 09 2017 - 09:30:03 PDT
