VMD-L Mailing List

From: Vermaas, Josh (vermaasj_at_msu.edu)
Date: Mon Feb 01 2021 - 10:40:27 CST

If you wanted to be more systematic, you could script something through ParmEd, loading your topology, and all the parameters you are allowing yourself to consider. My recollection is that ParmEd will tell you what is missing when you try to write out an Amber prmtop file.

-Josh

From: <owner-vmd-l_at_ks.uiuc.edu> on behalf of "Gumbart, JC" <gumbart_at_physics.gatech.edu>
Date: Monday, February 1, 2021 at 11:35 AM
To: SHIVAM TIWARI <t.shivam_at_iitg.ac.in>
Cc: Vmd l <vmd-l_at_ks.uiuc.edu>
Subject: Re: vmd-l: how to search for existing topology

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!sFfoUTYWf4kcvXj1JPssETaO2lH177NN0S786dQM-shXyWYWCITYnE7YCpV78Dnbrw$ <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!sFfoUTYWf4kcvXj1JPssETaO2lH177NN0S786dQM-shXyWYWCITYnE7YCpVJo4np0Q$ <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