[gmx-users] RNA woes

[Ken Rotondi]

Hello all,

I've two questions. One pretty straight forward, one quite puzzling. I 
am attempting to run pdb2gmx on a molecule with RNA and protein in it. 
Gromacs returns the following output/error message:

> There are 4 chains and 0 blocks of water and 3214 residues with 65787 
> atoms
>
>   chain  #res #atoms
>   1 'A'  2849  61325
>   2 'B'   120   2573
>   3 'C'   201   1542
>   4 'D'    44    347
>
> All occupancy fields zero. This is probably not an X-Ray structure
> boilerplate stuff
> Fatal error: Atom O5' in residue GUA 1 not found in rtp entry with 27 
> atoms
>              while sorting atoms

First (straight forward) question: the ffG43a2.rtp file has the atoms 
labeled as e.g. O5*, C5* while the .pdb file uses a O5', C5' 
convention. Is it possible to alter the .rtp file to O5' rather than 
editing the entire .pdb file, or will this lead to consequences with 
atom definitions in other files or programs.

Second (enigmatic) question:
The output states that there are 4 chains, there are in fact 16 chains.

It says that there are 2849 residues in chain A, there are 2902, 
however there are 51 residues numbered ##A, ##B, and 2902-51(2851) is 
tantalizingly close to 2849, and I can't be sure that I didn't miss 2 
residues in the 92,000+ lines. Why is it that in chain 1 the gromacs 
number (2849) seem to = actual # - alpha modified #

it says there are 120 residues in chain B, there are 119. In this case 
there is one residue numbered ##A. I've checked this one closely, no 
missing numbers, no other alphabetic modifiers. Why in chain 2 does the 
gromacs number (120) = actual number 119 + alpha modified AA's (1)

chain C has no alpha modified AA's and has 201 residues in both the 
.pdb and the gromacs output.

Chain D has no alpha modified AA's gromacs = 44 res. pdb file = 194 res

Chains E-P no gromacs output what-so-ever.

I'm attaching some relevant lines of the .pdb files to show that there 
appears to be no weirdness in the file (other than the alpha 
modifiers).

As always, any and all help is dearly appreciated.

Thanks in advance,

Ken

ATOM  90592  O3' URA A2849     -10.342 167.296 376.561
ATOM  90593  P   ADE A2850      -9.402 167.717 377.842

ATOM  92266  H2' CYT A2902      -7.209 248.135 339.137
TER
ATOM  92267  H5T URA B   1      57.009 198.578 207.741

ATOM  99289  OT2 LYS C 203     -22.338 199.866 326.683 (chain C starts 
at 3)
TER
ATOM  99290  N   ILE D   9     114.526 221.775 305.427

ATOM  99881  O   ARG D  44      93.740 197.779 316.513
ATOM  99882  N   ARG D  45      92.120 197.895 314.938

ATOM 102369  OT2 PHE D 202     119.421 206.618 298.441
TER
ATOM 102370  N   LEU E   7      37.107 135.878 199.523