[gmx-users] puzzled by unexpected [ bonds ] section resulting from running gmx x2top

[Jose Borreguero]

Victory! The -noparam did the trick :)
Thanks a million.

On Wed, Jun 21, 2017 at 11:43 AM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 6/21/17 11:39 AM, Jose Borreguero wrote:
>
>> Hi Justin,
>>
>> ​Thanks for your quick reply! ​
>> This means x2top is not finding
>> ​
>> or using
>> the right force constant value, right?
>> ​ I
>>
>> ​
>> did
>>   add the bond info into file ffbonded.itp
>> ​of
>> the oplsa.ff/ directory
>> ​
>> (https://goo.gl/z5UMot)
>> .
>> I also included the types in file
>> atomtypes.atp
>> ​
>>   and the non bonded info in
>> ffnonbonded.itp file. Maybe related to this issue is this line also found
>> in the output .top file:
>> ​    ​
>> #include "
>> ​​
>> ./oplsaa.ff/forcefield.itp"
>> This line should not be necessary because the .top​ file contains all
>> information. Does the line mean that the bond information in the output
>> .top file is overridden with that gmx later finds under
>> ​
>> ./oplsaa.ff
>> ​?
>> ​ If so, then the particular value of the force constant in the .top file
>> would  be irrelevant and my problem would be solved! :)
>>
>>
> Any value found in the .top overrides the force field.  Any blank in the
> topology is referenced from ffbonded.itp.  Anything missing after that
> generates a fatal error in grompp.  Use -noparam when running x2top if
> everything is accounted for in the force field parameter files.
>
>
> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
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