Hi,
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
check
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)??
Thanks
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Received on Fri Jan 16 2009 - 01:12:48 PST
