Re: Re: Chain identifiers in NAMD simulation

Date: Thu Apr 07 2022 - 21:11:42 CDT

Hi, JC,

The support of ff19SB was implemented in an internal branch (/haochuan_chen/5522) of gitlab and has not been merged to the master branch yet. If another version of NAMD is used, the CMAP terms are simply ignored without a warning in the simulation.

From: Gumbart, JC
Date: 2022-04-08 02:36
CC: Hrishikesh Dhondge
Subject: Re: namd-l: Chain identifiers in NAMD simulation

It should be mentioned that NAMD does not support the CMAP term of ff19SB

Why is this? Unless I’m mistaken, we’ve used ff19SB in NAMD before.


On Apr 6, 2022, at 7:17 AM, wrote:

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,
<namd-l_ Chain identifiers in NAMD simulation(1).eml>

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