From: Nathan Kern (
Date: Mon Feb 01 2021 - 11:06:18 CST

If you don't know the residue name in the CHARMM FF, you can often find the
correct name with CHARMM-GUI Ligand Reader & Modeler
<*ligandrm__;Lw!!DZ3fjg!uFeanaCvcUaTdht5XcIyP0KaR3d8FK_Lz0v1JIMHKvT8OTtrAFGp6SAPZZuOsGsXmg$ > using the "find similar
residues in CHARMM FF" option. It uses a maximum-common subgraph search
method to compare the actual molecular structures to each other.

On Mon, Feb 1, 2021 at 11:25 AM Gumbart, JC <>

> Honestly, I often do search the full set of topology files first, which
> you can download from here:;!!DZ3fjg!uFeanaCvcUaTdht5XcIyP0KaR3d8FK_Lz0v1JIMHKvT8OTtrAFGp6SAPZZukjxXrAg$
> <;!!DZ3fjg!u8S-rGoLZNQ1pvorBkq3czaDXu9Dtv7s0Os4PTD2dIQ3G5T2HaolO-Hm8tVPgibGhQ$>
> You can also run your compound through ParamChem to see how well CGenFF
> covers it:;!!DZ3fjg!uFeanaCvcUaTdht5XcIyP0KaR3d8FK_Lz0v1JIMHKvT8OTtrAFGp6SAPZZumT6P8Vg$
> <;!!DZ3fjg!u8S-rGoLZNQ1pvorBkq3czaDXu9Dtv7s0Os4PTD2dIQ3G5T2HaolO-Hm8tU5V7hvjw$>
> Note, this is *only* the general force field and does not include the
> highly optimized protein, lipid, etc. parameters.
> Best,
> JC
> On Jan 31, 2021, at 7:22 AM, SHIVAM TIWARI <> wrote:
> Dear all,
> This is regarding topology tutorial, a particular line is like this
> "bonding an O atom to CG would require choosing a type for the O atom,
> which is impossible, since there is no topology entry with O bonded to a
> proline or proline-like ring. We simply do not have parameters for oxygen
> bonded to a 5-member proline ring."
> This brings a question in my mind that, how one will know a priori whether
> a particular topology exist in CHARMM or not, ok the above case is a simple
> one, in a way that it belongs to the standard amino acid. But, what if my
> molecule, let us say contains some parts which are not amino acids. How do
> I search all the existing topological information in CHARMM force field and
> not just protein topology.
> regards
> shivam