Hi,
I am new in amber and i run a minimization like this:
antechamber -i mol.mol2 -fi mol2 -o mol.prepi -fo prepi -c bcc -nc 0
parmchk -i mol2.prepi -f prepi -o mol2.frcmod
xleap -s -f $AMBERHOME/dat/leap/cmd/leaprc.ff03
>source leaprc.gaff
>loadamberprep ./mol.prepi
>loadamberparams ./mol.frcmod
>check MOL
>saveamberparm x.prmtop x.inpcrd
sander -O -i min.in -o x.out -p x.prmtop -c x.inpcrd -r x.rst
min.in look lake this
&cntrl
imin = 1,
maxcyc = 10000,
ncyc = 5000,
ntb = 0,
igb = 0,
ntc = 2,
ntf = 2,
cut = 12,
/
My FINAL RESULTS look =
NSTEP ENERGY RMS GMAX NAME NUMBER
10000 4.1105E+02 3.0132E+00 1.7689E+01 H117 14
BOND = 2.6696 ANGLE = 17.0783 DIHED = 158.3704
VDWAALS = -37.1515 EEL = -631.0683 HBOND = 0.0000
1-4 VDW = 32.3588 1-4 EEL = 868.7910 RESTRAINT = 0.0000
Is it an obligation to obtain a negative ENERGY else in what kind of simulation we must have a negative energy ???
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Received on Sun Feb 01 2009 - 01:08:12 PST
