[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
>
> ========================================
> --
> gmx-users mailing list gmx-users at gromacs.org
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