[gmx-users] Micelle Modeling

[Justin A. Lemkul]

Janowicz, Adrianna C. wrote:
> I used your tutorial but am getting the error message
> 
> WARNING 1 [file dpc.top, line 28]:
>   18915 non-matching atom names
>   atom names from dpc.top will be used
>   atom names from dpc.gro will be ignore
> 
> probably because my .top file was generated using a file generated thru
> PRODRG (only inputing 23 DPC molecules and then specifying 65 of those
> units) while the .gro file was created using the whole .pdb file of the
> micelle containing all 65 units. How can I fix this error? -maxwarn 1
> doesn't seem to be doing the trick.
> 

I don't completely understand what you've done.  PRODRG uses a single molecule 
to produce a topology that can then be #included in the system topology.  I 
don't know how you inputted 23 molecules and then specified 65.  What does this 
mean?

Also note that PRODRG topologies are usually insufficiently accurate for actual 
use in simulations:

http://www.gromacs.org/Downloads/Related_Software/PRODRG#Tips

The source of the error could be one of several problems, please see:

http://www.gromacs.org/Documentation/Errors#XXX_non-matching_atom_names

-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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