[gmx-users] RNA ffG43a2.hdb problems

[Ken Rotondi]

All,

The problem was with the number after the nucleotide name in the first 
line of each residue type. The number is the number of hydrogen types, 
not number of hydrogens. Therefore, the correct entries for RNA 
nucleotides in the ffG43a2.hdb are:

ADE	2
	1	2	O2*	C2*	C3*
	2	3	N6	C6	N1
CYT	2
	1	2	O2*	C2*	C3*
	2	3	N4	C4	N3
GUA	3
	1	2	O2*	C2*	C3*
	2	3	N2	C2	N1
	1	1	N1	C6	C2
URA	2
	1	2	O2*	C2*	C3*
	1	1	N3	C2	C4

Ken


On Jan 19, 2005, at 4:07 PM, Ken Rotondi wrote:

> 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:
>
> ADE	3
> 	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:
>
> CYT	3
> 	1	2	O2*	C2*	C3*
> 	2	3	N4	C4	N3
> GUA	4
> 	1	2	O2*	C2*	C3*
> 	2	3	N2	C2	N1
> 	1	1	N1	C6	C2
> URA	2
> 	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.
>
> Ken
>
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