[gmx-users] Micelle Modeling

[Justin A. Lemkul]

Janowicz, Adrianna C. wrote:
> 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)
> 

I replicated the error.  The original coordinate file names its water hydrogens 
as HW2 and HW3 rather than HW1 and HW2, as expected by most common water models. 
  It is safe to ignore this error.

-Justin

> 
> 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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> 
> 
> 

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

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

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