[gmx-users] Atom types for phosphate group in OPLS-AA force field

Delmotte, Antoine antoine.delmotte09 at imperial.ac.uk
Thu Apr 26 18:15:33 CEST 2012

Thank you very much for your answer. This has been very helpful. I think 
I will follow your advice and try to find similar molecules to find the 

Could I just ask you if you know of a database where I could look for 
the opls parameters which have calculated for other molecules?

Best regards,


On 26/04/12 16:55, Justin A. Lemkul wrote:
> On 4/26/12 11:37 AM, Delmotte, Antoine wrote:
>> Dear Justin,
>> Many thanks for your response. I managed to reduce the number of 
>> errors by
>> trying other atom types, by looking at what seemed most likely to be 
>> right from
>> the ffnonbonded.itp and ffbonded.itp files.
>> Unfortunately, I did not manage to find a combination that both made 
>> some sense,
>> and allowed to remove the errors. So I guess these things need to be
>> parametrized, as you said.
>> Could you possibly let me know if there is a relatively easy and 
>> straightforward
>> way to find these parameters? (I guess the answer is probably "no", 
>> but it's
>> always worth asking, I guess...)
> You can make a first effort by assigning parameters based on existing, 
> similar, parameters.  They may or may not exist.
>> I also noticed that there is a option "-zero" in grompp which "Sets 
>> parameters
>> for bonded interactions without defaults to zero instead of 
>> generating an error".
>> What does it mean exactly? Is it just taking the angles and distances 
>> inferred
>> from the structure as the ones at equilibrium? Is it safe to use it?
> What it means is "ignore the problem and simply assign the value of 
> zero for equilibrium lengths, force constants, etc."
>> I am just a beginner with MD, and I just want to do a quick run to test
>> something. I have no need for super high accuracy, and the run I want 
>> to try
>> will be very small (maybe 1 or 2 ns, or something like that), and for 
>> a very
>> large system (~80 000 atoms). Would that be unreasonable to use that 
>> "-zero"
>> option (it is tempting, I must say...)?
> I say that using -zero is a bad idea.  It ignores the problem and 
> whatever results you obtain would be questionable, at best.  
> Parameterization of novel species is an advanced topic.  Most people 
> will spend several months developing good parameters for a new residue 
> or molecule.
> -Justin

More information about the gromacs.org_gmx-users mailing list