Dear Amber users,
I have run TI simulation on a system using pmemd (which needs single parmtop and inpcrd), I have in one state bonded disulphide bridge (state A) and in the other free cysteines (State B).
As I understand, CYX is recognised as bonded and CYS as free cysteine in amber, hence the partial charges are adjusted accordingly. Since free cysteines have an extra atom (HG), should these be added as a dummy atom to the bonded cysteines??
This is how I made the input files for running MD:
1) leap file
source leaprc.protein.ff14SB
source leaprc.water.tip3p
loadAmberParams frcmod.ionsjc_tip3p
m1 = loadpdb new_ss.pdb
m2= loadpdb new.pdb
bond m1.4.SG m1.30.SG
bond m1.15.SG m1.37.SG
bond m1.19.SG m1.39.SG
bond m2.4.SG m2.30.SG
bond m2.15.SG m2.37.SG
protein = combine {m1 m2}
set default nocenter on
solvateoct protein TIP3PBOX 15.0
savepdb protein protein_combine.pdb
saveamberparm protein protein_sol.parm7 protein_sol.rst7
quit
2) Timerge
parmed protein_sol.parm7 <<_EOF
loadRestrt protein_sol.rst7
setOverwrite True
tiMerge :1-40 :41-80 :19,39 :59,79
outparm merged_protein.parm7 merged_protein.rst7
quit
_EOF
3)Minimisation using the merged_protein.parm7 merged_protein.rst7
&cntrl
imin = 1, ntmin = 2, maxcyc = 2000, ncyc=1000,
ntpr = 20, ntwe = 20,
dx0 = 1.0D-7,
ntb = 1,
iwrap = 1,
icfe = 1, ifsc = 1, clambda = %L%, scalpha = 0.5, scbeta = 12.0,
logdvdl = 0,
timask1 = ':19,39',
timask2 = ':41,42',
scmask1 = ':19,39',
scmask2 = ':41,42',
!method 2:
!scmask1 = ':19,39', scmask2 = ':41,42',
/
&ewald
/
Looking forward to some comments on this.
Thanks in advance
Regards
Sowmya
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Received on Fri Feb 02 2018 - 02:30:02 PST
