Re: [AMBER] free energy of solvation of small molecules

From: Hannes Loeffler <>
Date: Wed, 25 Nov 2015 10:16:34 +0000

Dear Fabian.

if the authors have used GAFF you should be able to obtain the same
atoms types. Charges will of course vary depending on the derivation
method you use. Principally free energies are dependent on force field
parameters but I won't be able to tell you how much that would be
(there are a few papers out there which compare e.g. GAFF to OPLS).

A few points to check:
Reduce reads a dictionary of known PDB structures so make sure that
your PDB file does indeed name the ligand as SKF. Check reduce's
output to make sure that is true. Make sure that the hydrogens you
have obtained are the same as in the paper. If so you should get the
same atom types.

The charge models used for the AMBER family of force fields is
basically RESP or AM1/BCC (there are some exceptions but look that up
in the manual).


On Wed, 25 Nov 2015 11:43:36 +0200
Fabian gmail <> wrote:

> Dear Hannes,
> I am trying to reproduce initially the results from the Kaus et al
> paper you mention for the first ligand
> ( 7-sulfamoyl-1,2,3,4-tetrahydroisoquinolinium), now if I am
> understand correctly first I need to obtain the mol2 file using
> antechamber with gaff model, starting from the PDB structure of this
> ligand this is what I tried to do using this commands:
> reduce SKF_A.pdb > SKF_hyd.pdb
> antechamber -i SKF_hyd.pdb -fi pdb -o SKF.mol2 -fo mol2 -c bcc -s 2
> This yields completely different atom types and charges as compared
> to the paper of Kaus, as expected since they used RESP model and I
> used AMB1-BCC, but I don’t have gaussian….
> Do you think the final DG value will be highly different using the
> bcc model or could you recommend to use a different model of those
> included in amber that I could use, which will provide more similar
> charges to the ones on the paper?
> Will those values highly impact the final results?

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Received on Wed Nov 25 2015 - 02:30:04 PST
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