VMD-L Mailing List

From: SHIVAM TIWARI (t.shivam_at_iitg.ac.in)
Date: Thu Mar 25 2021 - 04:28:36 CDT

related files : https://urldefense.com/v3/__https://drive.google.com/drive/folders/1gsWySzNkPL5miLiHJ5S8wPKc2tht9khB?usp=sharing__;!!DZ3fjg!u9k2bBp8jinkrKsCSVJn2DAJDOUXhaH6TmIbcgKPxl5GioGTfxo1F8p7kdcpwJYSJg$

Dear all,
I have a molecule (structure in the link above), which I want to parameterize. I ran the molecule through cgenff (stream file in the link above), the parameter section of the stream file contains almost no parameters for bonds and impropers and non-bonded parameters are also missing. Basically, my molecule contains two same peptide strands connected with some chemical entity in between them. The main issue is that:

some amino acids in the peptide part have methylated backbone nitrogen (HN replaced by a methyl group) : I tried to search for a similar topology but to no avail, the closest I could find was dimethyl formamide in cgenff topology where a nitrogen is connected to a methyl group, but another partner was a carbonyl carbon, and hence I guess can't be used.

I also found a similar question on charmm mailing list (https://urldefense.com/v3/__https://www.charmm.org/ubbthreads/ubbthreads.php?ubb=showflat&Number=32493&page=all__;!!DZ3fjg!u9k2bBp8jinkrKsCSVJn2DAJDOUXhaH6TmIbcgKPxl5GioGTfxo1F8p7kddWvVTz1g$ ). And suggestion for using alanine topology and parameters were given, but there the alpha carbon was methylated and in my case backbone nitrogen. so, any suggestions in this regard?

Apart from that, for the rest of my molecule, I am thinking of piecing it together from the existing topologies and I am going to use the following approach, please give your suggestions:

1) For terminals I found the CT2 patch to be appropriate one.

2) the O between two CH2, I found this part similar to ether ( may be dimethyl ether).

3) For aliphatic chains, I can use any linear aliphatic chain topology.

4) For carbonyl bonded to CH2, I can use glycine.

thank you

regards
shivam