Dear Amber,
This question is a little complicated, so let's summarize the
abbreviation of my TI-QMMM softcore potential test run first:
mask 0 mask 1
ligand only : TC2 => TCL
ligand + protein: TC2 with protein => TCL with protein
( 1.) In both "TCL" and "TCL with protein" softcore potentials
production run, a warning keeps popping out: "*QMMM of protein-ligand
complex: Unable to achieve self consistency. No convergence in SCF after
1000 steps. QMMM: Job will continue with unconverged SCF. Warning energies
QMMM: and forces for this step will not be accurate." and "* / *QMMM of
ligand : Unable to achieve self consistency* ....". I am aware that there
is the similar issue reported
before<
http://archive.ambermd.org/201010/0388.html>.
However, I didn't include any water in QM regions so I am not sure what
happen on my runs. *Interestingly, the other pair of softcore potential
jobs, "TC2" & "TC2 with protein" run perfectly without this warning. *
( 2.) The other issue is in the softcore potentials production run of
"TCL" and "TCL with protein". *The ligand's bonds stretch too far after
about 200ps of production run.*
(movie<
http://s1076.photobucket.com/albums/w454/happypsu4/?action=view¤t=no_protein_step_2_TCL.mp4>)
However, such a stretch-out happens around 200 ps later than the* "QMMM of
protein-ligand complex: Unable to achieve self consistency*" warning. So
it seems like ( 1. ) & ( 2. ) might be independent issues?
On the other hand, I originally thought this stretch-out might be due to
SHAKE failure. However, I found I turned SHAKE off in the whole softcore
potential related simulation. Then I thought it might be something wrong
with .prmtop and .inpcrd. However, in the non-softcore potential runs, the
same .prmtop and .inpcrd works pretty well and no any issue / warning. So
now I am quite confused. Could you give me some comments? The followings
are my results / input files.
mask 0 mask 1
ligand only : TC2 => TCL
(pressure<
http://i1076.photobucket.com/albums/w454/happypsu4/TC2_solvate_33_0_1_summary_pressure.png>/
energy<
http://i1076.photobucket.com/albums/w454/happypsu4/TC2_solvate_33_0_1_summary_energy.png>
/temperature<
http://i1076.photobucket.com/albums/w454/happypsu4/TC2_solvate_33_0_1_summary_TEMP.png>/
RMSD<
http://i1076.photobucket.com/albums/w454/happypsu4/TC2_solvate_33_0_1_summary_RMSD.png>/
movies<
http://s1076.photobucket.com/albums/w454/happypsu4/?action=view¤t=no_protein_step_2_TCL.mp4>
/.out<
https://dl-web.dropbox.com/get/Public/warning/TCL_solvate_33_prod_v1_l1.out?w=c9525407>
/ .prmtop<
https://dl-web.dropbox.com/get/Public/warning/TCL_solvate_33.prmtop?w=a56740a5>
/ .inpcrd<
https://dl-web.dropbox.com/get/Public/warning/TCL_solvate_33.inpcrd?w=0fb94d48>
)
ligand + protein: TC2 with protein => TCL with protein (pressure
/energy<
http://i1076.photobucket.com/albums/w454/happypsu4/FabI_NAD_TCL_wat_33A_1_1_summary_energy.png>
/temperature<
http://i1076.photobucket.com/albums/w454/happypsu4/FabI_NAD_TCL_wat_33A_1_1_summary_TEMP.png>/
RMSD<
http://i1076.photobucket.com/albums/w454/happypsu4/FabI_NAD_TCL_wat_33A_1_1_summary_RMSD.png>/
movies<
http://s1076.photobucket.com/albums/w454/happypsu4/?action=view¤t=with-FabI_step2.mp4>
/.out<
https://dl-web.dropbox.com/get/Public/warning/FabI_NAD_TCL_wat_33A_prod_v1_l1.out?w=73ec51e3>/
.prmtop<
https://dl-web.dropbox.com/get/Public/warning/FabI_NAD_TCL_wat_33A.prmtop?w=32ec69ca>/
.inpcrd<
https://dl-web.dropbox.com/get/Public/warning/FabI_NAD_TCL_wat_33A.inpcrd?w=d42729ec>
)
###################################The input file of "TCL with protein"
######################################
cat << EOF > mdin_min_v0_l${X}
FabI step 1 Minimization Therm Integ${X}: protein+ligand
&cntrl
imin = 1,
ntx = 1,
maxcyc = 2000,
ntmin = 2,
ntpr = 100,
ntf = 1,
ntc = 1,
ntb = 1,
cut = 10.0,
icfe = 1,
clambda =0.0092,
EOF
cp mdin_min_v0_l${X} mdin_min_v1_l${X}
cat << EOF >> mdin_min_v0_l${X}
ifsc=1,
crgmask='${mask0}',
scmask='${mask0}',
&end
EOF
cat << EOF >> mdin_min_v1_l${X}
ifsc=1,
crgmask='${mask1}',
scmask='${mask1}',
&end
EOF
cat << EOF > mdin_equi_v0_l${X}
FabI step 1 Equilibration 1 Therm Integ${X}: protein+ligand
&cntrl
imin = 0,
irest = 0,
ntx = 1,
ntb = 1,
cut = 10.0,
ntr = 1,
ntc = 1,
ntf = 1,
tempi = 0.0,
temp0 = 300.0,
ntt = 3,
gamma_ln = 2.0,
nstlim = 50000,
dt = 0.001,
ntpr = 250,
ntwx = 250,
ntwr = 2500,
icfe = 1,
clambda =0.0092
EOF
cp mdin_equi_v0_l${X} mdin_equi_v1_l${X}
cat << EOF >> mdin_equi_v0_l${X}
ifsc=1,
crgmask='${mask0}',
scmask='${mask0}',
/
Keep the Protein fixed with weak restraints
10.0
RES 1 258
/
END
END
EOF
cat << EOF >> mdin_equi_v1_l${X}
ifsc=1,
crgmask='${mask1}',
scmask='${mask1}',
/
Keep the Protein fixed with weak restraints
10.0
RES 1 258
/
END
END
EOF
cat << EOF > mdin_equi_v0_2${X}
FabI step 1 Equilibration 2 Therm Inter protein ligand
&cntrl
imin = 0,
irest = 1,
ntx = 5,
ntb = 2,
ntp = 1,
pres0 = 1.0,
taup = 2.0,
cut = 10,
ntr = 0,
ntc = 1,
ntf = 1,
tempi = 300.0,
temp0 = 300.0,
ntt = 3,
gamma_ln = 2.0,
nstlim = 50000,
dt = 0.001,
ntpr = 250,
ntwx = 250,
ntwr = 2500,
icfe = 1,
clambda =0.0092,
EOF
cp mdin_equi_v0_2${X} mdin_equi_v1_2${X}
cat << EOF >> mdin_equi_v0_2${X}
ifsc=1,
crgmask='${mask0}',
scmask='${mask0}',
&end
EOF
cat << EOF >> mdin_equi_v1_2${X}
ifsc=1,
crgmask='${mask1}',
scmask='${mask1}',
&end
EOF
cat << EOF > mdin_prod_v0_l${X}
NPT production
&cntrl
imin = 0,
ntx = 5,
irest = 1,
ntpr = 250,
ntwr = 2500,
ntwx = 250,
ntf = 1,
ntc = 1,
ntb = 2,
cut = 10.0,
nstlim = 600000,
dt = 0.001,
temp0 = 300.0,
ntt = 3,
gamma_ln = 2.0,
ntp = 1,
pres0 = 1.0,
taup = 2.0,
icfe = 1,
clambda =0.0092,
EOF
cp mdin_prod_v0_l${X} mdin_prod_v1_l${X}
cat << EOF >> mdin_prod_v0_l${X}
ifsc=1,
crgmask='${mask0}',
scmask='${mask0}',
ifqnt = 1
/
&qmmm
iqmatoms=3868,3869,3870,3871,3872,
3873,3874,3875,3876,3877,
3878,3879,3880,3881,3882,
3883,3884,3885,3886,3887,
3888,3889,3890,1395,1394,
1396,1398,1399,2328,2327,
3833,3834,3835,3836,3837,
3838,3839,3840,3841,3862,
3863,3864,3865,3866,3867
qmcharge=-1,
qm_theory='PM3',
qmshake=0,
qm_ewald=1, qm_pme=1
/
&end
EOF
cat << EOF >> mdin_prod_v1_l${X}
ifsc=1,
crgmask='${mask1}',
scmask='${mask1}',
ifqnt = 1
/
&qmmm
iqmatoms=3868,3869,3870,3871,3872,
3873,3874,3875,3876,3877,
3878,3879,3880,3881,3882,
3883,3884,3885,3886,3887,
3888,3889,3890,1395,1394,
1396,1398,1399,2328,2327,
3833,3834,3835,3836,3837,
3838,3839,3840,3841,3862,
3863,3864,3865,3866,3867
qmcharge=-1,
qm_theory='PM3',
qmshake=0,
qm_ewald=1, qm_pme=1
/
&end
EOF
Best,
Pin-Chih
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Received on Tue Aug 28 2012 - 17:00:02 PDT
