[gmx-users] Micelle Modeling
Justin A. Lemkul
jalemkul at vt.edu
Tue Jul 26 22:26:07 CEST 2011
Janowicz, Adrianna C. wrote:
> 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!!
>
These errors come up all the time, I'm surprised you haven't found the answers
in the archive.
With respect to the zero masses, it's because the [atoms] section does not list
masses, so they're set to zero. The proper format would have mass listed in the
column to the right of charge. The reason it's missing is because the topology
posted online is for (1) an ancient version of Gromacs (probably in the 3.x
series) and (2) for use with the deprecated ffgmx force field, which had some
different internal mechanics. Note that this is not a reason to use ffgmx
(please refer to the manual for the full explanation as to why you shouldn't use
it).
The missing parameters are also probably due to similar issues. I believe you
said you were using my tutorial as a basis for your simulations, so you'll have
to make all the parameters conform to the 53a6 nomenclature. For instance, atom
type OS was replaced by either OE or OA, depending on the functional group.
You'll have to update the topology accordingly. There are probably other such
issues, as well.
-Justin
>
>
> 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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>
>
>
--
========================================
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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