AMBER Archive (2009)

Subject: RE: [AMBER] bad energy??!!

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Wed Jan 14 2009 - 13:40:24 CST

Hi Momo,

The issue of positive energies has been discussed many times before on this
list. For example:

http://archive.ambermd.org/200803/0088.html

Essentially the origin for classical molecular mechanics calculations is
arbitrary. It is also not the same for two different molecules. Hence there
is nothing inherently wrong with a positive energy.

I suggest taking a look at some introductory text books on classical force
fields.

All the best
Ross

> -----Original Message-----
> From: amber-bounces_at_ambermd.org [mailto:amber-bounces_at_ambermd.org] On
> Behalf Of momo momo
> Sent: Wednesday, January 14, 2009 11:19 AM
> To: amber_at_ambermd.org
> Subject: [AMBER] bad energy??!!
>
>
> 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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