[gmx-users] Micelle Modeling

Janowicz, Adrianna C. ajanow3 at uic.edu
Tue Jul 26 22:16:21 CEST 2011


thanks! one last problem:
Im using the dpc.itp file & I keep getting an error having a problem with
the 0 mass for the atoms 11-23 (I've searched forums & haven't found
anyone having a problem with the 0 masses), along with   No default Proper
Dih. types,  No default Bond types  No default Ryckaert-Bell. types &  No
default LJ-14 types!!



DPC.itp from UCalgary site:
    1     CH3       1    DPC      C1       1         0.4	; qtot: 0.248
     2     CH3       1    DPC      C2       1         0.4	; qtot: 0.496
     3     CH3       1    DPC      C3       1         0.4	; qtot: 0.744
     4      NL       1    DPC      N4       1        -0.5	; qtot: 0.752
     5     CH2       1    DPC      C5       1         0.3	; qtot: 1
     6     CH2       1    DPC      C6       1         0.4	; qtot: 1
     7      LOS       1    DPC      O7       1        -0.8	; qtot: 0.64
     8       P       1    DPC      P8       1         1.7	; qtot: 1.64
     9      OM       1    DPC      O9       1        -0.8	; qtot: 1
    10      OM       1    DPC     O10       1        -0.8	; qtot: 0.36
    11      LOS       1    DPC     O11       1        -0.7	; qtot: 0
    12     CH2       1    DPC     C12       5             0	; qtot: 0
    13     CH2       1    DPC     C13       6             0	; qtot: 0
    14     CH2       1    DPC     C14       7             0	; qtot: 0
    15     CH2       1    DPC     C15       8             0	; qtot: 0
    16     CH2       1    DPC     C16       9             0	; qtot: 0
    17     CH2       1    DPC     C17      10             0	; qtot: 0
    18     CH2       1    DPC     C18      11             0	; qtot: 0
    19     CH2       1    DPC     C19      12             0	; qtot: 0
    20     CH2       1    DPC     C20      13             0	; qtot: 0
    21     CH2       1    DPC     C21      14             0	; qtot: 0
    22     CH2       1    DPC     C22      15             0	; qtot: 0
    23     CH3       1    DPC     C23      16             0	; qtot: 0




On Tue, July 26, 2011 1:16 pm, Justin A. Lemkul wrote:
>
>
> 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
>
> ========================================
> --
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