[gmx-users] RNA ffG43a2.hdb problems

Ken Rotondi ksr at chemistry.umass.edu
Wed Jan 19 22:07:17 CET 2005

Hello all,

I had a copy of this post go off into the ether ~ an hour ago, so here 
goes again...

I'm trying to run RNA w/ the gromos FF. Upon running pdb2gmx on the rna 
file (with the -ignh flag) I received the following errors:

WARNING: atom H2* is missing in residue ADE x in the pdb file
          You might need to add atom H1* to the hydrogen database of 
residue ADE
          in the file ff???.hdb (see the manual)

3 such errors in ADE, 3 in CYT, 4 in GUA	and 2 in URA to be exact. I 
read the manual and added the following to the end of the ffG43a2.hdb 
file in my working directory:

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

to account for the H2* hydroxy proton on the ribose ring and the 2 
amine hydrogens on N6 or the purine ring, respectively.

Re-running pdb2gmx resulted in WARNINGs only for CYT, GUA and URA, ADE 
was fixed, apparently. So, I added:

	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

for the hydrogens of the other nucleotides.

Upon re-running pdb2gmx I received the following error:

Opening library file ffG43a2.hdb
Fatal error: wrong format in input file ffG43a2.hdb on line
CYT     3

I shuffled the ADE, CYT, GUA and URA entries extensively, it was ALWAYS 
the second nucleotide that generated the error. I opened the .hdb file 
with vi and I could see no reason why there was a difference. I opened 
a copy in MSWord to see if all the paragraph and tab signatures were 
the same amongst the nucleotides and the other molecules. They were. I  
tried placing the 4 nucleotides at the beginning of the .hdb file. Same 
behavior, the first nucleotide is okay, subsequent ones generate the 
fatal error (I again shuffled them around).

So, what am I missing? Why does only the first nucleotide register 
correctly while subsequent ones don't, regardless of the nucleotide 
order or where they are in the file (beginning or end)? I could really 
use some help/insight here.


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