*Dear All,*
*I am modifying tutorial A9 for thermodynamic integration with GPU. **(I
already completed tutorial A9, so Amber installation might not cause the
following problem.)*
*I downloaded the protein structure (PDB ID: IBNI), and*
*I would like to make a mutation from ALA032 to CYS032. *
*(because it starts VAL003, I changed it to VAL001. ALA032 is the 30th
position in protein structure).*
*Before Amber 18 TI simulation, I prepared the protein structure with
schrodinger maestro suite (OPLS3 force field).*
<1b-leap.sh>
m1 = loadpdb $basedir/1BNI_min.pdb
mC = loadpdb $basedir/1BNI_A032C_min.pdb
proteinC = combine {m1 mC}
set default nocenter on
# create protein in solution
solvatebox proteinC TIP3PBOX 12.0 0.75
# set
savepdb proteinC proteinC.pdb
<2_eliminate_duplicates>
$parmed proteinC.parm7 <<_EOF
loadRestrt proteinC.rst7
setOverwrite True
tiMerge :1-108 :109-216 :30 :138
outparm merged_proteinC.parm7 merged_proteinC.rst7
quit
_EOF
*In TI simulation, there are three steps (min - heat - ti).*
*In the first step (min in 0.0 window), I got the following output message.*
NSTEP ENERGY RMS GMAX NAME NUMBER
1 -8.5820E+09 2.3340E+05 8.3854E+06 SG 1708
BOND = 50.8558 ANGLE = 365.8724 DIHED =
1175.2357
VDWAALS = ************* EEL = -82033.0023 HBOND =
0.0000
1-4 VDW = 339.2536 1-4 EEL = 4440.2756 RESTRAINT =
0.0000
DV/DL = **************
Softcore part of the system: 10 atoms, TEMP(K) =
0.00
SC_Etot= 0.0000 SC_EKtot= 0.0000 SC_EPtot =
37.4610
SC_BOND= 0.3313 SC_ANGLE= 1.2445 SC_DIHED =
14.1283
SC_14NB= 0.3001 SC_14EEL= 37.1542 SC_VDW =
-0.1308
SC_EEL = -15.5665
SC_RES_DIST= 0.0000 SC_RES_ANG= 0.0000 SC_RES_TORS=
0.0000
SC_EEL_DER= *********** SC_VDW_DER= *********** SC_DERIV =
***********
------------------------------------------------------------------------------
*I think the *********** problem caused 'STOP PMEMD Terminated Abnormally'
error message.*
*I attached my input files for test simulation.*
*What causes the * *********** *problem in output message?*
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- application/octet-stream attachment: heat.in
- application/octet-stream attachment: min.in
- application/octet-stream attachment: ti.in
Received on Sat Oct 05 2019 - 03:00:02 PDT
