[gmx-users] no default bond for the defined 'SPECBOND'

[Justin Lemkul]

On 10/19/17 9:10 AM, Li, Tong wrote:
> Dear all,
>
> I am developing the top file for a polymer using the force field of 54a7. The top files for the head/tail and repeating monomers are well developed and they are working fine. The bond between different monomers is defined in 'sepcbond.dat', however, cannot be recognized as a default bond that has pre-defined parameters. Is there a way to modify the 'ffbond.itp' file to include the needed information? I used to change it in opls-aa, but cannot do it in the 54a7 force field as the force field parameters are defined in a different way.

The ffbonded.itp file simply contains parameters for bonds, it has 
nothing to do with which bonds are actually supposed to be formed in a 
given molecule. That's what the .rtp and specbond.dat files are for. If 
you did not get the bond you expected, that means you did not set the 
right criteria for having that bond formed. Note that the reference 
distance in specbond.dat has a tolerance of +/- 10% and if the 
coordinates are outside that range, you won't get a bond formed.

-Justin

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

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jalemkul at vt.edu | (540) 231-3129
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