[gmx-users] Missing Interactions in [ angles ] Section in Topology

[Justin A. Lemkul]

Lara Bunte wrote:
> Hi
> 
> In some lines the equilibrium angle and the force constant is missing.I give you an example:
> 
> 
> The [ angles ] section is build like
> 
> [ angles ]
> ;  ai    aj    ak funct            c0            c1            c2            c3
>    2     1    19     1    123.75     250.00
>     1     2    3      1    123.75     250.00
>     1     2    4      1    117.47     230.00
> 
> 
> 
> And my pdb2gmx output is for example something like
> 
> [ angles ]
> ;  ai    aj    ak funct            c0            c1            c2            c3
>     2     1    19     1    123.75     250.00
>     1     2     3      1   
> 
>     1     2     4      1    117.47     230.00
> 
> 

So you have a complete topology and one that has missing parameters, or are you 
adapting an incomplete topology?

What force field are you using?  What is the system?  For a normal protein 
system, most force fields (all except Gromos, if I recall) produce bonded 
directives with no parameters; they are looked up from ffbonded.itp and not 
stated explicitly, so "missing" parameters are completely normal and not 
problematic.  If you're dealing with something nonstandard and you've had to 
create .rtp entries, you'll need to post that information for diagnostic purposes.

In principle, there's nothing wrong with any of this.  The blank lines will be 
filled in with existing parameters from [angletypes] in ffbonded.itp.  These 
parameters are only overwritten if explicitly present in the topology.  If there 
is a bonded interaction referenced in the topology that does not exist in 
ffbonded.itp, grompp will fail with a fatal error.

-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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