Dear AMBER users,
I run minimization and ALPB (implicit) for my system, and I got ***** in my
results. However, the process is still running without any termination.
Taking a look at the result out file, I found the energy values very high
and making no sense. But I was wondering why it still goes on!
May I know what causes those signs? Isn't it caused by the clashes in the
structures or the structure was not properly minimized? (I did manually
added some residues at the C-terminus using PyMOL before running LEAP)
*Some parts in my "min.out":*
*--------------------------------------------------------------------------------
4.
RESULTS--------------------------------------------------------------------------------
NSTEP ENERGY RMS GMAX NAME NUMBER
1 1.0192E+09 2.3921E+03 2.9622E+04 CD2 2173 BOND
= 2098.2191 ANGLE = 1879.9662 DIHED =
7231.0827 VDWAALS = ************* EEL = -29805.1123 EGB =
-3969.0885 1-4 VDW = 1748.9921 1-4 EEL = 18601.0877 RESTRAINT
= 0.0000 NSTEP ENERGY RMS GMAX
NAME NUMBER 50 7.8969E+09 1.5515E+03 2.4066E+04
CD 1879 BOND = 10054.8295 ANGLE = 3361.2589 DIHED
= 7365.2000 VDWAALS = ************* EEL = -29868.6478
EGB = -3964.7021 1-4 VDW = 1889.2111 1-4 EEL =
18580.3036 RESTRAINT = 0.0000 NSTEP ENERGY
RMS GMAX NAME NUMBER 100 1.7369E+04
1.1784E+01 5.6167E+02 CB 1957 BOND = 8325.7619
ANGLE = 7502.5986 DIHED = 7821.6785 VDWAALS =
6259.6519 EEL = -29799.2679 EGB = -3921.2607 1-4 VDW
= 2803.6005 1-4 EEL = 18375.8932 RESTRAINT = 0.0000*
*And this is in my alpb.out:*
*--------------------------------------------------------------------------------
4.
RESULTS--------------------------------------------------------------------------------
NSTEP
= 0 TIME(PS) = 0.000 TEMP(K) = 362.66 PRESS =
0.0 Etot = 973.8494 EKtot = 5892.6038 EPtot =
-4918.7545 BOND = 3649.7039 ANGLE = 1271.3646 DIHED
= 6715.5822 1-4 NB = 1261.5081 1-4 EEL = 18050.3786
VDWAALS = -1941.5065 EELEC = -29963.4263 EGB =
-3962.3591 RESTRAINT =
0.0000 ------------------------------------------------------------------------------
NSTEP
= 50000 TIME(PS) = 100.000 TEMP(K) = 304.32 PRESS =
0.0 Etot = 4620.7597 EKtot = 4944.6138 EPtot =
-323.8541 BOND = 4747.8715 ANGLE = 3564.4840 DIHED
= 7334.7221 1-4 NB = 1418.4182 1-4 EEL = 18058.7550
VDWAALS = -1566.9135 EELEC = -29668.8880 EGB =
-4212.3034 RESTRAINT =
0.0000 ------------------------------------------------------------------------------
NSTEP
= 100000 TIME(PS) = 200.000 TEMP(K) =********* PRESS =
0.0 Etot = ************** EKtot = ************** EPtot =
2013386.2788 BOND = -0.0000 ANGLE = 2060779.5162 DIHED
= 30593.7121 1-4 NB = 0.0000 1-4 EEL = 0.0001
VDWAALS = 0.0000 EELEC = -0.0094 EGB =
-77986.9402 RESTRAINT =
0.0000 ------------------------------------------------------------------------------*
*My min.in <
http://min.in>:*
#running minimization for the whole system
&cntrl
imin=1,
maxcyc=5000,
ncyc=2500,
ntb=0, igb=5,
ntr=0,
cut=999.0
/
*My alpb.in <
http://alpb.in>:*
&cntrl
imin=0,
irest=0, ntx=1,ig=-1,
igb=5, saltcon=0.2, alpb=1, arad=29.21,
ntb=0,
ntxo=2,
cut=999.0,
ntc=2,
ntf=2,
tempi=300.0,
temp0=300.0,
ntt=3,
gamma_ln=1.0,
nstlim=50000000,
dt=0.002,
ntpr=50000,
ntwx=50000,
ntwr=50000
/
Please help comment. Thank you.
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Received on Mon Aug 17 2015 - 00:00:04 PDT
