Re: [gmx-users] gen_pairs to calculate absent 1-4 interactions in CHARMM36c FF

Peter C. Lai pcl at
Fri Apr 27 23:39:24 CEST 2012

btw you only need explicit 1-4 for charmm when the 1,4 from the original charmm prm is actually different/specified (i.e. non-conjugated carbons) 
Sent from my Android phone with K-9 Mail. Please excuse my brevity.

"Ricardo O. S. Soares" <ross_usp at> wrote:

Hi Mark,

yeah, I'll try it. 

Thanks for your reply,


De: Mark Abraham <Mark.Abraham at>
Para: Discussion list for GROMACS users <gmx-users at> 
Enviadas: Sexta-feira, 27 de Abril de 2012 10:43
Assunto: Re: [gmx-users] gen_pairs to calculate absent 1-4 interactions in CHARMM36c FF

On 27/04/2012 5:21 AM, Ricardo O. S. Soares wrote: 

Dear users,

In GROMACS, does CHARMM36 ff, calculate eventual 1-4 interactions that are absent from the [pairtypes] section of the ffnonbonded.itp file?

I ask this because I'm converting cholesterol parameters from CHARMM36c to gmx format, and several 1-4 values are absent in the last two columns of the prm file.

Does setting gen_pairs to "yes" in the [defaults] section in the forcefield.itp work?

Probably. What documentation exists is probably in the walk-through example of manual 5.7.1. You can probably construct yourself a trivial test case if you wish to verify how things work.


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