[gmx-users] Micelle Modeling

[Janowicz, Adrianna C.]

Im sorry for the confusion.
I used an .itp file from the UCalgary site for dpc, I input a line

[ molecules ]
; molecule name nr.
DPC 65
SOL 6305

in the dpc.top file.

However, I generated the .gro file directly from the m65.pdb file from the
UCalgary site using the editconf command.

>> WARNING 1 [file dpc.top, line 28]:
>>   18915 non-matching atom names
>>   atom names from dpc.top will be used <=(taken from 1 dpc.itp x 65)
>>   atom names from dpc.gro will be ignore <=(made from 65 dpc molecule pdb)


On Mon, July 25, 2011 8:21 am, Justin A. Lemkul wrote:
>
>
> 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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