From: Smith, Harper E. (
Date: Thu Jan 28 2021 - 14:36:52 CST

Hi Eddie,

There are N/C terminal patches you can apply to your residue. One idea might be to acetylate the N-terminus (patch ACE) and methylamidate the C-terminus (patch CT3).

From: <> on behalf of Prof. Eddie <>
Sent: Thursday, January 28, 2021 3:21 PM
To: Peter Freddolino <>
Cc: Vmd l <>
Subject: Re: vmd-l: novel residue creation and parameterization

The novel residue attaches to the carbon alpha of the backbone just as any sidechain so there is nothing funky there. But if I make a fragment of just the sidechain to save then some bonds need to get left out and so this is what causes the problem. If I include the backbone I have "dangling" bonds there. If I try just the sidechain I have a dangling bond there. I don't see how without inputting the complete protein I can avoid that, but I can't see how using the whole protein is reasonable either. How can I give cgenff something that doesn't have a dangling bond then? Do I have to treat it as a ligand and add hydrogens to terminate say the backbone atoms and then manually remove those from the topology file?
Thanks again for your help!

On Thu, Jan 28, 2021 at 12:24 PM Peter Freddolino <<>> wrote:
Hi Eddie,
You certainly shouldn't be parameterizing the whole protein, only the new residue that you're trying to add. What is the chemistry of the attachment of your new component to the rest of the protein? Is it incorporated to the protein backbone in some way, or is it a modification attached to a side chain? The protein topologies are by design pretty modular, so what you just need to figure out is what is an appropriate attachment point beyond which you can treat your new component like any other part of the protein force field. Just for example, if you were trying to add a new amino acid, you would likely assume (unless the beta carbon had some really funky chemistry) that you can use the same backbone parameters as all other amino acids in the charmm forcefield, and then focus on parameterizing your fragment and its attachment to the alpha carbon.
Best, Peter

On Thu, Jan 28, 2021 at 12:32 PM Prof. Eddie <<>> wrote:
I'm not sure how to do that. Molfracture saves each residue in its own mol2 file. Otherwise, I need to rename the whole protein to have 1 residue name. Even then cgenff says I have a carbene and won't proceed (although molfracture does not find anything which a large charge). Is there some other way to write it?

Also, do I need the whole protein put into cgenff or is there a way to just have my novel residue and have it ignore the (incomplete) backbone? I would just like to get the files so I can use fftk (which may also be difficult if I need the whole protein in gaussian instead of just the novel residue)--_000_CH2PR01MB5639D6FCAD4FC68218B263F8FABA9CH2PR01MB5639prod_--