[gmx-users] RNA ffG43a2.hdb problems

Ken Rotondi ksr at chemistry.umass.edu
Wed Jan 19 20:52:05 CET 2005

I'm still trying to get the gromos forcefield to work w/ RNA.

Upon running pdb2gmx on my rna file the following warnings resulted

WARNING: atom H61 is missing in residue ADE x in the pdb file
	You might need to add atom H61 to the hydrogen database of residue ADE
	in the file ff???.hdb (see the manual)

etc. for CYT, GUA and URA

So okay, I saw the manual and added the following to the end of my 
ffG43a2.hdb file:

	1	2	O2*	C2*	C3*
	2	3	N6	C6	N1

and re-ran pdb2gmx. The warnings for ADE were gone, while those for 
CYT, GUA and URA persisted. I thought I was on the right track. So I 

	1	2	O2*	C2*	C3*
	2	3	N4	C4	N3
	1	2	O2*	C2*	C3*
	2	3	N2	C2	N1
	1	1	N1	C6	C2
	1	2	O2*	C2*	C3*
	1	1	N3	C2	C4

to the .hdb file and re-ran pdb2gmx. My output was:

Fatal error: wrong format in file ffG43a2.hdb on line

I've shuffled the hydrogen data for the 4 nucleotides and it ALWAYS 
reads the first one correctly and returns the above fatal error for 
whichever nucleotide is second. I've looked at the file with vi and see 
no difference between any of the nucleotides and the other entries. I 
even opened it with MSWord and checked that the tab and return 
characters were the same amongst the nucleotides as well as with the 
other molecules.

I could really use some help on this. Again, this seems like it must be 
a simple problem, but I'm not seeing the solution.

Thank you,


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