[gmx-users] [ pairs ] section in topology

[Justin A. Lemkul]

Lara Bunte wrote:
> Hi
> 
> My topology file which I get after pdb2gmx has in one section following section:
> 
> [ pairs ]
> ;  ai    aj funct            c0            c1            c2            c3
>     1     5     1
>     1     6     1
>     1     9     1
>     1    17     1
> 
> 
> Is it correct that there are no entries in c0, c1, c2 and c3? What is the problem? 
> 

There is no problem.  Pair parameters are referenced from [pairtypes] in 
ffnonbonded.itp or otherwise generated if gen-pairs is set to "yes" in the 
[defaults] directive of the force field.

-Justin

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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