AMBER Archive (2009)

Subject: [AMBER] bad energy??!!

From: momo momo (
Date: Wed Jan 14 2009 - 13:19:20 CST

I study a comlexation between two molecule, after i generate the prmtop and inpcrd files like this;

 antechamber -fi mol2 -i mol1.mol2 -fo prepi -o mol1.prepi -c bcc -s 2
 parmchk -i mol1.prepi -f prepi -o mol1.frcmod

antechamber -fi mol2 -i mol1.mol2 -fo prepi -o mol2.prepi -c bcc -s 2

 parmchk -i mol2.prepi -f prepi -o mol2.frcmod

xleap -s -f $AMBERHOME/dat/leap/cmd/leaprc.ff03
> source leaprc.gaff
    loadamberprep mol1.prepi
    loadamberparams mol1.frcmod
    loadamberprep mol2.prepi

    loadamberparams mol2.frcmod
    edit MOL1
    unit> import MOL2
    alignaxes MOL1
    saveamberparm MOL1 xx.prmtop xx.inpcrd

I do LMOD calculation and i found a positive energy like this:

Full liste:

 1 E 126.743 / 1 Rg = 2.5771

Is there any probleme or there is correct ( positive energy)??

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