[gmx-users] Fatal Error: Atom N not found in building block 1DA . . .

Justin Lemkul jalemkul at vt.edu
Tue Nov 20 00:50:50 CET 2018

On 11/19/18 3:50 PM, Austin Biaggne wrote:
> Hi All,
> I’m aware this issue has come up and been answered many times, but after reading through numerous threads regarding it and trying different solutions I am still having trouble finding a solution.
> I am trying to simulate a DNA strand (built using Chimera) by going through the same process as in the Lysozome  tutorial. The first time around I used CHARMM27 and everything worked fine and I was able to complete an MD run. But upon using CHARMM36 as has been done in literature, I received the error “Fatal error: atom N not found in building block 1DA while combining tdb and rtp” when running the command:
> “gmx pdb2gmx -f dna.pdb -o processed.gro -water spce”
>   Going through the files within CHARMM27 and CHARMM36, I could not find any discrepancies between the .tdb and .rtp files that would cause this error, other than in CHARMM36 the .rtp and .tdb are merged. Unless I am horribly mistaken about the changes between CHARMM27 and CHARMM36, I am unsure why 27 would work and not 36.

The force fields are organized differently. The C36 port is 
auto-generated from a much larger set of CHARMM force field files, and 
functionally it is very difficult to split things into well-defined 
protein, DNA, RNA, etc. files. So we don't and we just merge things into 
one big .rtp file. Hence the user has to make some more choices.

> Reading through previous threads regarding this issue, I tried using “-ter” to specify termini (selecting None as well as the other options), to no avail. To my knowledge, the .pdb, .rtp, and .tdb files are setup correctly (I am

Well, what did you pick when you specified -ter? This is precisely what 
you have to do, and you need to pick the appropriate nucleic acid 
termini, 5TER and 3TER, for the 5'- and 3'-termini. This is actually the 
*only* choice that you can currently make for C36 with nucleic acids in 



Justin A. Lemkul, Ph.D.
Assistant Professor
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Virginia Tech Department of Biochemistry
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