[gmx-users] "No default proper Dih.type

[Justin A. Lemkul]

varsha gautham wrote:
> Dear all,
> 
> Am trying to do simulation of DPPC membrane.Am using ffgmx force 
> field,because other force fields doesnt have DPP residue,so got an error 
> saying "Residue DPP not in topology database.
> 

Don't use ffgmx for anything.  It is long-since deprecated.  The parameters that 
Tieleman offers at his site are the most widely-used in simulations of 
membranes, and reproduce experimental observables quite well:

http://moose.bio.ucalgary.ca/index.php?page=Structures_and_Topologies


> So i generated topology file using pdb2gmx -ff gmx -f inp.pdb -o out.gro
> 
> now after few more steps i updated topology again to run grompp..
> 
> on grompp am getting an error saying

For these types of errors, go into the topology and look at the line that's 
giving the error.  Map those atom numbers back onto your structure to see where 
the problem is.  If no such dihedral exists within the ff*bon.itp file, then you 
have a problem.  Otherwise, you have to specify the parameters yourself.

But as I said, stop and get better parameters first.

-Justin

> 
> "ERROR 0 [file "topol.top", line 30026]:
>   No default Proper Dih. types
> ERROR 0 [file "topol.top", line 30027]:
>   No default Proper Dih. types
> ERROR 0 [file "topol.top", line 30066]:
>   No default Proper Dih. types
> ERROR 0 [file "topol.top", line 30067]:
>   No default Proper Dih. types
> ERROR 0 [file "topol.top", line 30106]:
>   No default Proper Dih. types
> ERROR 0 [file "topol.top", line 30107]:
>   No default Proper Dih. types
> ERROR 0 [file "topol.top", line 30146]:
>   No default Proper Dih. types
> ERROR 0 [file "topol.top", line 30147]:
>   No default Proper Dih. types
> ERROR 0 [file "topol.top", line 30186]:
>   No default Proper Dih. types
> ERROR 0 [file "topol.top", line 30187]:
>   No default Proper Dih. types
> ERROR 0 [file "topol.top", line 30226]:
>   No default Proper Dih. types
> ERROR 0 [file "topol.top", line 30227]:
>   No default Proper Dih. types
> ERROR 0 [file "topol.top", line 30266]:
>   No default Proper Dih. types
> ERROR 0 [file "topol.top", line 30267]:
>   No default Proper Dih. types
> ERROR 0 [file "topol.top", line 30306]:
>   No default Proper Dih. types
> ERROR 0 [file "topol.top", line 30307]:
>   No default Proper Dih. types
> ERROR 0 [file "topol.top", line 30346]:
>   No default Proper Dih. types
> ERROR 0 [file "topol.top", line 30347]:
>   No default Proper Dih. types
> ERROR 0 [file "topol.top", line 30386]:
>   No default Proper Dih. types
> ERROR 0 [file "topol.top", line 30387]:
>   No default Proper Dih. types
> ERROR 0 [file "topol.top", line 30426]:
>   No default Proper Dih. types
> ERROR 0 [file "topol.top", line 30427]:
>   No default Proper Dih. types
> ERROR 0 [file "topol.top", line 30466]:
>   No default Proper Dih. types
> ERROR 0 [file "topol.top", line 30467]:
>   No default Proper Dih. types
> ERROR 0 [file "topol.top", line 30506]:
>   No default Proper Dih. types
> ERROR 0 [file "topol.top", line 30507]:
>   No default Proper Dih. types
> ERROR 0 [file "topol.top", line 30546]:
>   No default Proper Dih. types
> ERROR 0 [file "topol.top", line 30547]:
>   No default Proper Dih. types
> ERROR 0 [file "topol.top", line 30586]:
>   No default Proper Dih. types
> ERROR 0 [file "topol.top", line 30587]:
>   No default Proper Dih. types
> ERROR 0 [file "topol.top", line 30626]:
>   No default Proper Dih. types
> ERROR 0 [file "topol.top", line 30627]:
>   No default Proper Dih. types
> ERROR 0 [file "topol.top", line 30666]:
>   No default Proper Dih. types
> ERROR 0 [file "topol.top", line 30667]:
>   No default Proper Dih. types
> ERROR 0 [file "topol.top", line 30706]:
>   No default Proper Dih. types
> ERROR 0 [file "topol.top", line 30707]:
>   No default Proper Dih. types
> ERROR 0 [file "topol.top", line 30746]:
>   No default Proper Dih. types
> ERROR 0 [file "topol.top", line 30747]:
>   No default Proper Dih. types
> ERROR 0 [file "topol.top", line 30786]:
>   No default Proper Dih. types
> ERROR 0 [file "topol.top", line 30787]:
>   No default Proper Dih. types
> ERROR 0 [file "topol.top", line 30826]:
>   No default Proper Dih. types
> ERROR 0 [file "topol.top", line 30827]:
>   No default Proper Dih. types
> ERROR 0 [file "topol.top", line 30866]:
>   No default Proper Dih. types
> ERROR 0 [file "topol.top", line 30867]:
>   No default Proper Dih. types
> ERROR 0 [file "topol.top", line 30906]:
>   No default Proper Dih. types
> ERROR 0 [file "topol.top", line 30907]:
>   No default Proper Dih. types
> ERROR 0 [file "topol.top", line 30946]:
>   No default Proper Dih. types
> ERROR 0 [file "topol.top", line 30947]:
>   No default Proper Dih. types
> ERROR 0 [file "topol.top", line 30986]:
> 
> 
> Please help me out in this issue.Thanks in advance..
> 
> -krithika
> 
> 
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-- 
========================================

Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================