Date: Mon, 23 Sep 2024 08:09:41 +0000
Dear Amber users and developers,
just wanted to ask you about one detail:
I carried out constant pH MD in explicit solvent, ASP, GLU, HIS and CYS were included in the list of titratable residues (the former 3 were renamed in AS4, GL4 and HIP, accordingly) and pH was set to 7.35.
cpinutil.py -igb 2 -resnames HIP AS4 GL4 CYS -p cpH_prot_RC_tip3p18oct_hmr.prmtop -op cpH_prot_RC_tip3p18oct_hmr_cpi.prmtop -o cpH_prot_RC_tip3p18oct_hmr.cpin
the mdin file was:
&cntrl
imin = 0, nstlim = 125000000, dt = 0.004,
irest = 1, ntx = 5, ig = -1,
temp0 = 300.0, icnstph=2,
ntcnstph=100, ntrelax=200, solvph=7.35,
ntc = 2, ntf = 2,
ntwx = 12500, ntwr = 12500, ntpr = 2500,
cut = 9.0, iwrap = 1, saltcon=0.15,
ntt =3, gamma_ln=2.0, ntb = 1, ntp = 0,
nscm = 1000,
ioutfm=1, ntxo=2,
/
I applied the HMR technique as well.
Having performed analysis after 500ns, I found that the cysteines underwent no transition and remained all the time in SH state; then I carried out the simulation 80ns long at pH=8.5 and again no transitions of CYS into anion were observed. From literature it is known that one CYS can have unusually low side-chain pKa.
I guess some additional work-around for cysteines should have been done...
Can you please prompt me which one exactly?
Kind regards
Nick
Computational chemistry and
molecular modeling
The Nancy and Stephen Grand Israel National Center for Personalized Medicine
Weizmann Institute of Science
M +972 52 7439671
234 Herzl Street, P.o. Box 26,
Rehovot, 7610001 Israel
[1694421514730]
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