VMD-L Mailing List

From: Gumbart, JC (gumbart_at_physics.gatech.edu)
Date: Mon Feb 01 2021 - 09:57:27 CST

Honestly, I often do search the full set of topology files first, which you can download from here: https://urldefense.com/v3/__http://mackerell.umaryland.edu/charmm_ff.shtml__;!!DZ3fjg!u8S-rGoLZNQ1pvorBkq3czaDXu9Dtv7s0Os4PTD2dIQ3G5T2HaolO-Hm8tVPgibGhQ$

You can also run your compound through ParamChem to see how well CGenFF covers it: https://urldefense.com/v3/__https://cgenff.umaryland.edu/__;!!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 <t.shivam_at_iitg.ac.in<mailto:t.shivam_at_iitg.ac.in>> 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