[gmx-users] Topologies and charges for large organic ligands

[Dean Cuebas]

Dear colleagues,

In 53a6, the topology and charges for (NAD+) nicotinamide adenine
dinucleotide are present (listed as NADH, 52 atoms) in polar hydrogen form
(without aromatic hydrogens).

Is there anyone who can tell me how such a molecule was charge group
parameterized? (with sufficient certainty to be included in the ff).

Please understand that I am not asking how to use the NAD topology that's
provided.

I've read that prodrg is a good starting point for parametrizing a ligand,
but what is the path to improving such a ligand from that starting point?
(the provided topology for NAD+ in the ff shows 17 charge groups with
an average of 3-4 atoms per charge group, whereas prodrg gives only 11
charge groups.)

I'm not concerned about angles and dihedrals, since that is pretty
painless... it's the charge groups that I'm concerned about.

In a nutshell, who and how was the final NAD+ parameters decided upon??
Does anyone know this??  Is it simply chemical intuition of estimated
charges that reproduce the dipole of the moiety (like an adenine ring), and
the charge groups contain the minimum number of atoms that reflect this?

Is there an algorithm to generating improved charge groups?

I ask these questions because my ligands are large organics... MW 800 and
greater.

Thanks for any and all help in this regard.

-- 
Dr. Dean Cuebas, Associate Prof of Chemistry
deancue...@smsu.edu, Ph 417-836-8567 FAX 417-836-5507
Dept. of Chemistry, Southwest Missouri State University
Springfield, Missouri 65804



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Re: [gmx-users] Topologies and charges for large organic ligands

[Ran Friedman]

Hi,

The answer is (or should be) in:

@article{Oostenbrink2004,
   Author = {Oostenbrink, C. and Villa, A. and Mark, A. E. and Van
Gunsteren, W. F.},
   Title = {A biomolecular force field based on the free enthalpy of
hydration and solvation: The GROMOS force-field parameter sets 53A5 and
53A6},
   Journal = {J. Comput. Chem.},
   Volume = {25},
   Pages = {1656-1676},
   Year = {2004} }

Good luck,
Ran.

Dean Cuebas wrote:
 Dear colleagues,

 In 53a6, the topology and charges for (NAD+) nicotinamide adenine
 dinucleotide are present (listed as NADH, 52 atoms) in polar hydrogen form
 (without aromatic hydrogens).

 Is there anyone who can tell me how such a molecule was charge group
 parameterized? (with sufficient certainty to be included in the ff).

 Please understand that I am not asking how to use the NAD topology that's
 provided.

 I've read that prodrg is a good starting point for parametrizing a ligand,
 but what is the path to improving such a ligand from that starting point?
 (the provided topology for NAD+ in the ff shows 17 charge groups with
 an average of 3-4 atoms per charge group, whereas prodrg gives only 11
 charge groups.)

 I'm not concerned about angles and dihedrals, since that is pretty
 painless... it's the charge groups that I'm concerned about.

 In a nutshell, who and how was the final NAD+ parameters decided upon??
 Does anyone know this??  Is it simply chemical intuition of estimated
 charges that reproduce the dipole of the moiety (like an adenine ring), and
 the charge groups contain the minimum number of atoms that reflect this?

 Is there an algorithm to generating improved charge groups?

 I ask these questions because my ligands are large organics... MW 800 and
 greater.

 Thanks for any and all help in this regard.

   

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