Paracetamol is a very simple organic molecule, containing very usual chemical groups. The GAFF (General Amber Force Field) is very efficient in desrcibing the molecular mechanics of such simple molecules (read carefully the AmberTools manual in particular antechamber). The only aspect that would need a careful parametrization are the elctrostatic charges. You can use the R.E.D. Server to perform a standard RESP paramatrization, but if you have access to the Gaussian of to the GAMESS quantum-chemistry software you can easily perform the charge fitting by yourself.

Hello.

First of all, what is the software you are planning to use?

Best regards,

Ricardo Ferreira

Paracetamol is a very simple organic molecule, containing very usual chemical groups. The GAFF (General Amber Force Field) is very efficient in desrcibing the molecular mechanics of such simple molecules (read carefully the AmberTools manual in particular antechamber). The only aspect that would need a careful parametrization are the elctrostatic charges. You can use the R.E.D. Server to perform a standard RESP paramatrization, but if you have access to the Gaussian of to the GAMESS quantum-chemistry software you can easily perform the charge fitting by yourself.

I agree with Andrea Coletta. Also, I can suggest you to try GROMACS. You can generate topologies for small molecules with the ATB webserver (http://compbio.biosci.uq.edu.au/atb/) and get good parameters for gromos force field. Of course, all depends on what you want/need to do with your system! Good luck!

Hello.

I agree with Marcelo and Andrea. You also have PRODRG online server.

Best regards,

Ricardo Ferreira

What's your email address?

Marcelo an Riccardo are right... Gromacs topology is easier to modify... you can use acpype to convert Amber prmtop in gromacs format

This depends in which MM context you want to work. If you want a nice parameterizer for CHARMm and GROMACS. I warmly recommend swissparam http://www.swissparam.ch/ Paraetamol is far from being exotic so it should work without any problem. Enjoy!

Antoine.

Hi Ricardo, Im planning to use GULP to do the fitting of the potential. I'm looking at Dreiding to use as the force field. I'm trying to fit several paracetamol based structures i.e co-crystal,salt,polymorphs,hydrates and optimised the structure using the the refine Dreiding potential.

Andrea, Yes I agree that paracetamol is a simple organic molecule. Current software that i have access to are materials studio and Mercury. I'll look into your suggestion for GAFF. I will read the manual as im not familiar with it. Thanks for the suggestion. Will work on that straight away.

Dear all, I am trying to study paracetamol crystallization. I parametrized GAFF force field and I am using GROMACS. I have done some MD tests to see the stability of the crystal structure but even though I am simulating very big system size consist of 300 paracetamol in ethanol solution. crystal structure it is not stable and it start to dissolve very fast. however, experimentally, paracetamol crystallize in ethanol. As you correctly mentioned in your discussion, it is always important to know if the parameters are correct for the "purpose" of your study! At this point, I would like to check my force filed parameters. There are some experimental data available for paracetamol, such as solubility, melting temperature, crystal structure and ...! Since I have never done such as study, I would like to know your comments about it!

Many thanks

Fahimeh

Dear Fahimeh,

Could you obtain a stable crystals of other substances? I have heard that the modeling of crystallization is a very difficult task.

Alexey, Indeed it is a difficult task mainly because there are not valid force field parameters for studying crystallization... As you may know, force fields should be validated prior to use ... especially for small drugs such as paracetamol ....