[gmx-users] add a new bond to a force field
jalemkul at vt.edu
Wed Aug 8 21:00:57 CEST 2012
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 A. Lemkul, Ph.D.
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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