[gmx-users] Micelle Modeling

[Janowicz, Adrianna C.]

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.

Thanks,
Adrianna









On Tue, July 12, 2011 12:47 pm, Justin A. Lemkul wrote:
>
>
> Janowicz, Adrianna C. wrote:
>> Also, I forgot to mention that I need to throw a protein into the mix.
>> How
>> would I get both the protein and the DPC into the box?
>>
>>
>
> Have a look through some of the more advanced tutorials.  There is nothing
> that
> will walk you through all of it explicitly (and it's a LOT to put in an
> email),
> but you can probably piece it together:
>
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/index.html
>
> Tutorial 2 is probably the most directly applicable.  Instead of a
> membrane you
> have a micelle, but the principle is the same.
>
> -Justin
>
>>
>>
>> On Tue, July 12, 2011 10:46 am, Justin A. Lemkul wrote:
>>>
>>> Janowicz, Adrianna C. wrote:
>>>> Users,
>>>> I'm trying to start a micelle modeling project & have tried countless
>>>> approaches to making a DPC micelle. My problems include:
>>>> -DPC not being recognized when I try to imput it into the [molecules]
>>>> seciton of the topology file to account for the DPC molecules in the
>>>> water
>>>> topology. Otherwise, the molecule #s do not match. (This approach
>>>> included
>>>> using a coordinate file for DPC & using the -nmol fuction in genbox to
>>>> place the DPC molecules into the water).
>>>>
>>>> I would appreciate any help. Even if this means taking a totally
>>>> different
>>>> approach in getting the DPC molecules into the box.
>>>>
>>> The best approach would be to:
>>>
>>> 1. Create the topology for a single molecule of DPC
>>> 2. Generate a configuration of the DPC micelle and edit the number of
>>> molecules
>>> in the .top appropriately
>>> 3. Solvate and let genbox add the correct number of water molecules to
>>> the
>>> .top
>>>
>>> -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
>
> ========================================
> --
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