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Compatibility of `XML` files with FF of MoSDeF and LigParGen?

#586ClosediGulitch 创建于 2024-09-24
I
iGulitchcommented
Hi, all! Trying to use `XML` file with FF generated by **LigParGen** in **foyer**, and obviously receive an error message. Checking the fields of foyer `XML` file with OPLS-AA FF and the **LigParGen**-generated `XML` FF file via `cat <file>.xml | sed -n '/<\//p'` and obtain for **foyer** : ``` </AtomTypes> </HarmonicBondForce> </HarmonicAngleForce> </RBTorsionForce> </NonbondedForce> </ForceField> ``` and for **LigParGen** : ``` </AtomTypes> </Residue> </Residues> </HarmonicBondForce> </HarmonicAngleForce> </PeriodicTorsionForce> </NonbondedForce> </ForceField> ``` There is the clear difference. Suppose, I remove `</Residue>` and `</Residues>`. But what remains different are `</RBTorsionForce>` from **foyer** : `<Proper class1="Br" class2="C" class3="CB" class4="CT" c0="0.0" c1="0.0" c2="0.0" c3="0.0" c4="0.0" c5="0.0"/>` and `</PeriodicTorsionForce>` from **LigParGen** : `<Improper class1="C841" class2="C840" class3="C842" class4="C843" k1="0.000000" k2="10.460000" k3="0.000000" k4="0.000000" periodicity1="1" periodicity2="2" periodicity3="3" periodicity4="4" phase1="0.00" phase2="3.141592653589793" phase3="0.00" phase4="3.141592653589793"/>` and these two clearly have different formats. Any idea / recommendation on how to merge the **LigParGen** `XML` file into the **foyer** `XML` ?
关闭于 2024-10-02 2 条评论