AMBER Archive (2009)

Subject: [AMBER] help

From: momo momo (m.o.m_at_live.fr)
Date: Fri Jan 30 2009 - 06:35:22 CST

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 ???

_________________________________________________________________
Découvrez Windows Live Spaces et créez votre site Web perso en quelques clics !
http://spaces.live.com/signup.aspx_______________________________________________
AMBER mailing list
AMBER_at_ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber