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

--
========================================

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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