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

Austin Biaggne austinbiaggne at u.boisestate.edu
Mon Nov 19 21:50:54 CET 2018

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.

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 very new to GROMACS so my knowledge is limited). There is one thread from 2011 that got to this point but after being asked to post the .pdb file, they never responded. 

I have attached a text document with the DA1 portion of the .pdb, followed by the DA portion of the .rtp from CHARMM36, followed by the contents of the .n.tdb from CHARMM36. Atom N is also defined in “atomtypes”.

Any insight would be appreciated!

Thanks in advance,

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