Re: Chain identifiers in NAMD simulation

Date: Wed Apr 06 2022 - 06:17:46 CDT

Hi, Hrishikesh Dhondge,

If you use CHARMM-GUI for modeling, then you will have a PDB file with chain and segment identifiers. Still, input files created by leap should also be fine.
It should be mentioned that NAMD does not support the CMAP term of ff19SB, so you can only use ff14SB for modeling at best.

Good luck,
From: Hrishikesh Dhondge
Date: 2022-04-06 18:00
To: namd-l
Subject: namd-l: Chain identifiers in NAMD simulation

I have a doubt regarding the simulation in NAMD. If I have to use the amber force field in NAMD, then I can create the system in the leap program provided by AMBER. But the leap program renumbers the residues in the simulation system. Chain identifiers are not used. There is a single list of all atoms where atoms and residues are numbered sequentially starting from 1 without any gaps.

So if I have a protein-RNA/DNA complex to simulate, will it affect the simulation (missing information about chain or segment identifiers)?

Thanks in advance!

With regards
Hrishikesh Dhondge
PhD student,

This archive was generated by hypermail 2.1.6 : Tue Dec 13 2022 - 14:32:44 CST