[gmx-users] Complication of errors, .itp file regarding

[Justin Lemkul]

On 12/17/17 2:54 PM, RAHUL SURESH wrote:
> Dear all
>
> I managed to overcome above errors by manually creating an .itp file from
> the parameter file of ffTK. But i end up with 139 warnings stating
>
>
>
>
> *"Too few parameters on line (source file
> /home/viji/Downloads/Gromacs/gromacs-2016.4/src/gromacs/gmxpreprocess/toppush.cpp,
> line 1841) "*
> Going through previous threads, the error arise because I have used atom
> type instead of numbers in bond and angle section of .itp file. To change
> all the names to number is really a difficult task ( though not impossible
> ) and take lot ground work and much much time. I would like to know if
> something can be done actually to create an itp through some script which
> are already available, rather dumping all my time over this renumbering
> process. Please sort out some better way.
>

Sounds like you have a totally broken topology. Solve the first issue 
you posted and to which I responded; it's much simpler to deal with.

-Justin

>
>
> On Mon, 18 Dec 2017 at 12:41 AM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>>
>> On 12/17/17 8:18 AM, RAHUL SURESH wrote:
>>> Dear all
>>>
>>> Let me put forth the thing first. I have generated the parameter file
>> using
>>> fftk(structure.par) and derived the respective topology
>> file(structure.top)
>>> using topotools of vmd. Now to get the itp fiule, I manually copied the
>>> necessary data from structure.top and made structure.itp file.
>>>
>>> For the command
>>> * "gmx grompp -f em.mdp -c solv.gro -p alz.top -o ions.tpr"*
>>>    I get so many warning and errors.
>>>
>>> WARNING 1 [file THC.itp, line 3]:
>>>     Overriding atomtype CG2D1
>>>
>>> WARNING 31 [file THC.itp, line 37]:
>>>     Overriding Bond parameters.
>>>
>>> WARNING 35 [file THC.itp, line 111]:
>>>     Overriding U-B parameters.
>>>
>>> *69 warning messages*
>>>
>>> ERROR 1 [file THC.itp, line 158]:
>>>     Encountered a second block of parameters for dihedral type 9 for the
>> same
>>>     atoms, with either different parameters and/or the first block has
>>>     multiple lines. This is not supported.
>> The above errors are due to the fact that your molecule's .itp file
>> includes parameters that are already part of the parent force field,
>> hence grompp overrides them with the second instance. Don't do this. If
>> an interaction is already specifically parametrized and is part of the
>> force field, use it. Remove duplicated parameters from your .itp file.
>>
>>> *47 error messages*
>>>
>>> and finally
>>>
>>>
>>>
>>>
>>>
>>> *Fatal error:number of coordinates in coordinate file (solv.gro,
>>> 31285)             does not match topology (alz.top, 31330)*
>>> Please make it simple.
>> The answer to this problem is always the same - incorrect bookkeeping.
>> Check your work starting from addition of solvent and count how many of
>> each species there are to make sure you've done things correctly.
>>
>> -Justin
>>
>> --
>> ==================================================
>>
>> Justin A. Lemkul, Ph.D.
>> Assistant Professor
>> Virginia Tech Department of Biochemistry
>>
>> 303 Engel Hall
>> 340 West Campus Dr.
>> Blacksburg, VA 24061
>>
>> jalemkul at vt.edu | (540) 231-3129
>> http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
>>
>> ==================================================
>>
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-- 
==================================================

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

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