[gmx-users] add a new bond to a force field

[Justin Lemkul]

On 8/8/12 2:58 PM, Shima Arasteh wrote:
>
>
> Dear gmx friends,
>
> I'm supposed to add a bond not defined in bond-types by default. I used cgenff and got the bond parameters as this:
>
> CG2O1  HGR52   317.13     1.1000 ! FORM, formamide reverted to value from par_all22_prot.inp and par_cgenff_1d.inp
>
> I know the atomtypes are not in agreement, so modified it as :
> C          H           317.13     1.1000 ! FORM, formamide reverted to value from par_all22_prot.inp and par_cgenff_1d.inp
>
>
> Now should I add this parameters directly to the bondtypes section in ffbonded.itp file of charmm36 FF? Does this line need to be modified anymore?
>

That line cannot be used directly.  The units are wrong and thus require 
conversion.  Presumably, if the atom types (not names) are used and the values 
are in the correct order and have the right units, that's all you need to do.

-Justin

-- 
========================================

Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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