Hi Thomas,
Thank you for your help. The question you asked is exactly what I want to say. I can manually modify the prmtop file to make sure that 'GAFF-particles' use AMBER combine rules and 'OPLS-particles' use OPLS combine rules. However, I don't know how to set up the LJ parameters between 'GAFF-particles' and 'OPLS-particles'.
Regarding the website you gave me (
http://virtualchemistry.org/index.php), I read the article by Dr. Spoel et al (Carl Caleman, Paul J. van Maaren, Minyan Hong, Jochen S. Hub, Luciano T. Costa and David van der Spoel Force Field Benchmark of Organic Liquids: Density, Enthalpy of Vaporization, Heat Capacities, Surface Tension, Isothermal Compressibility, Volumetric Expansion Coefficient, and Dielectric Constant, J. Chem. Theor. Comput., 8, 61-74 (2012).DOI). They found that the organic solvents with OPLS force field generate slightly better properties than those with GAFF. So I want to model benzonitrile with OPLS force field.
Sincerely,
Guoxiong
On Feb 21, 2012, at 8:38 AM, Thomas Schlesier wrote:
> I'm not familiar with AMBER, but mixing two force field is usually not a
> good idea.
> Concerning the comination-rules for LJ:
> If you could use both combination-rules and each force field uses only
> its own rule it would be fine for the interactions between particles of
> each force field.
> But you will run into problems, if an 'OPLS-particle' interacts with a
> 'GAFF-particle' -> what combination rule one should use?!?
> Think the easiest way would to use also GAFF for benzonitrile.
> You could look here:
> http://virtualchemistry.org/index.php
> They have some solvents for GAFF (and also OPLS).
>
> Greetings
> Thomas
>
>
> Am 20.02.2012 22:56, schrieb Guoxiong Su:
>> Hi AMBER experts,
>>
>> I am trying to solvate a molecular triad in a benzonitrile box. For this molecular triad, I used Antechamber to generate the topology file with GAFF. The charge is calculated using AM1-BCC. I have done some literature search and I found OPLS force filed has the parameters for benzonitrile. Is it reasonable to mix GAFF with OPLS force field in AMBER?
>>
>> I have read though the mailing list and I found some people was mixing AMBER force field with the Glycam force field (e.g. http://archive.ambermd.org/200906/0240.html). I knew that for GAFF, SCNB = 2.0 and SCEE = 1.2. What values are they in OPLS? Is it 1.0 since OPLS doesn't have any scaling? The combine rules of GAFF and OPLS for the Lennard-Jones potentials are different as well. GAFF follows the AMBER rules and OPLS uses geometric mean for sigma and epsilon. Is it possible to use two kinds of combine rules in AMBER?
>>
>> Thank you for your help in advance.
>>
>> Sincerely,
>> Guoxiong Su
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Received on Tue Feb 21 2012 - 09:00:02 PST
