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

[Justin Lemkul]

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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