Re: Re: AMBER: F,Cl,Br,I in MMPBSA

From: Yong Xu <>
Date: Fri, 21 Oct 2005 9:12:15 +0800

Dear Prof. Case

thank you for you reply on the question of F,Cl,Br,I in MMPBSA!

I encounter other problems when I calculate solvation energies of some small molecules

when I use xleap to generate, lig.crd and lig.pdb, xleap can't give out correct lig.pdb.
I perform following step before I do xleap work.

give a ligand's MOL2 file, lig.mol2
antechamber -i lig.mol2 -fi mol2 -o lig.gjf -fo gcrt

g98 <lig.gjf> lig.out
I didn't use "opt" in lig.gjf, so the geometry SHOULD still be the same as lig.mol2 file

antechamber -i lig.out -fi gout -o lig.prep -fo prepi -c resp
parmchk -i lig.prep -f prepi -o lig.frcmod

then I use following script to perform xleap.
/local/amber7/exe/xleap <<EOF
source /local/amber7/dat/leap/cmd/leaprc.gaff
source /local/amber7/dat/leap/cmd/leaprc.ff99
loadamberprep ./lig.prep
loadamberparams ./lig.frcmod
saveamberparm MOL lig.crd
savepdb MOL lig.pdb

I viewed lig.pdb and found that the geometry is very strange with some unexpected connection.

please find the enclosed file: no222_1.* (.gjf .out .crd .top .pdb .prep .frcmod )

======= 2005-10-17 08:10:00 David A. Case wrote=======

>On Wed, Oct 12, 2005, Yong Xu wrote:
>> I want to do some MMPBSA work on a series of small molecules composed of F,
>> Cl, Br, or I atoms. but there are no parameter for those elements.
>These atoms have not been parameterized in the Amber scheme (as far as I
>know), but the "Bondi" radii should give good starting points:
> A. Bondi
> J. Chem. Phys.
> 64
> 441
> 1964
>Maybe some list-members who have done large scale calculations can pitch in
>with ideas. Note that the only thing "missing" are parameters for the surface
>area part (please let me know if I am wrong here), and I don't think that
>small uncertainties in the parameters for halogens would lead to much overall
>uncertainty in the final results: getting good charges (and therefore good C-X
>bond dipoles) is probably much more important.
>The AMBER Mail Reflector
>To post, send mail to
>To unsubscribe, send "unsubscribe amber" to

= = = = = = = = = = = = = = = = = = = =

Best regards!
        Yong Xu


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Received on Fri Oct 21 2005 - 02:53:02 PDT
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