Hello Everyone
I am calculating relative binding affinity of two ligands using TI. In
vdw_decoupling step (protein medium). Till heating everything went fine, but
I am facing this error at the beginning of the equilibration "vlimit
exceeded for step Coordinate resetting (SHAKE) cannot be accomplished,
deviation is too large". In mailing archive I found that increasing the box
size might solve this problem. I tried with box size of 10, 12 and 14 A box
size, but this error is occurring every time. Can anyone please guide me how
to get rid of this error?
During heating the water box is getting bit deformed, but the temperature
scaling and energy graphs are very fine, also the protein as well as ligand
structures are maintained properly without any bond stretching...etc.
Also the same ligands are running fine (water medium), without any error
Below is the heating and equilibration file pasted:
heatres1_$lambda
Heating
&cntrl
imin = 0, irest = 0, ntx = 1, ntb = 1, cut = 10, ntr = 1,
nmropt = 1, ntc = 2, ntf = 1, tempi = 0.0, temp0 = 300.0,
ntt = 3, gamma_ln = 1.0, nstlim = 60000, dt = 0.002, ntpr = 100, ntwx =
1000, ntwr = 1000, icfe=1, clambda=$lambda, klambda=1.0, ifsc = 1, crgmask=
':DRG.N33,C34,O35,C36,C37,C38,C39,C40,C41,C42,O43,N44,C45,C46,H47,H48,H49,H50,H51,H52,H53,H54,H55,H56',
scmask = ':DRG.N33,C34,O35,C36,C37,C38,C39,C40,C41,C42,O43,N44,C45,C46,H47,H48,H49,H50,H51,H52,H53,H54,H55,H56',
nscm = 2000, ntave=5000,
/
&wt TYPE='TEMP0', istep1=0, istep2=45000,
value1=0.1, value2=300.0, /
&wt TYPE='DUMPFREQ',ISTEP1=10, /
&wt TYPE='END' /
Hold the DRG fixed
5.0
RES 1 292
END
END
heatres2_$lambda
Heating
&cntrl
imin = 0, irest = 0, ntx = 1, ntb = 1, cut = 10, ntr = 1,
nmropt =1, ntc = 2 ntf = 1, tempi = 0.0, temp0 = 300.0,
ntt = 3, gamma_ln = 1.0, nstlim = 60000, dt = 0.002, ntpr = 100, ntwx =
1000, ntwr = 1000, icfe=1, clambda=$lambda, ifsc = 1,
crgmask=':DRG.C33,C34,S35,C36,C37,C38,N39,C40,C41,N42,C43,C44,S45,O46,C47,O48,H49,H50,H51,H52,H53,H54,H55,H56,H57,H58,H59,H60,H61,H62',
scmask = ':DRG.C33,C34,S35,C36,C37,C38,N39,C40,C41,N42,C43,C44,S45,O46,C47,O48,H49,H50,H51,H52,H53,H54,H55,H56,H57,H58,H59,H60,H61,H62',
klambda=1.0, nscm = 2000, ntave=5000,
/
&wt TYPE='TEMP0', istep1=0, istep2=45000,
value1=0.1, value2=300.0, /
&wt TYPE='DUMPFREQ',ISTEP1=10, /
&wt TYPE='END' /
Hold the DRG fixed
5.0
RES 1 292
END
END
equi1_$lambda
Equilibration
&cntrl
imin = 0, irest = 1, ntx = 5, ntb = 2, pres0 = 1.0, ntp = 1,
taup = 1.0, cut = 10, ntr = 0, ntc = 2, ntf = 1, nrespa = 1,
tempi = 300.0, temp0 = 300.0, ntt = 3, gamma_ln = 1.0, tol = 0.000001,
nstlim = 250000, dt = 0.002, ntpr = 1000, ntwx = 10000, ntwr = 1000, icfe=1,
clambda=$lambda, klambda=1.0, nscm = 2000, ntave=5000, ifsc = 1, crgmask=
':DRG.N33,C34,O35,C36,C37,C38,C39,C40,C41,C42,O43,N44,C45,C46,H47,H48,H49,H50,H51,H52,H53,H54,H55,H56',
scmask = ':DRG.N33
,C34,O35,C36,C37,C38,C39,C40,C41,C42,O43,N44,C45,C46,H47,H48,H49,H50,H51,H52,H53,H54,H55,H56',
/
equi2_$lambda
Equilibration
&cntrl
imin = 0, irest = 1, ntx = 5, ntb = 2, pres0 = 1.0, ntp = 1,
taup = 1.0, cut = 10, ntr = 0, ntc = 2, ntf = 1, nrespa = 1,
tempi = 300.0, temp0 = 300.0, ntt = 3, gamma_ln = 1.0, tol = 0.000001,
nstlim = 250000, dt = 0.002, ntpr = 1000, ntwx = 10000, ntwr = 1000, icfe=1,
clambda=$lambda, klambda=1.0, nscm = 2000, ntave=5000, ifsc = 1,
crgmask=':DRG.C33,C34,S35,C36,C37,C38,N39,C40,C41,N42,C43,C44,S45,O46,C47,O48,H49,H50,H51,H52,H53,H54,H55,H56,H57,H58,H59,H60,H61,H62',
scmask = ':DRG.C33
,C34,S35,C36,C37,C38,N39,C40,C41,N42,C43,C44,S45,O46,C47,O48,H49,H50,H51,H52,H53,H54,H55,H56,H57,H58,H59,H60,H61,H62',
/
Thanks in Advance
Regards
--
--
SUNITA GUPTA
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Received on Wed Nov 24 2010 - 22:30:04 PST
