[gmx-users] RNA woes

[David van der Spoel]

On Wed, 2005-07-20 at 17:34 -0400, Ken Rotondi wrote:
> 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.
this you would do by editing the xlateat.dat file which translates atom
names.

> 
> Second (enigmatic) question:
> The output states that there are 4 chains, there are in fact 16 chains.
Have you used 16 different labels?

> 
> 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)
A chain identifier consists of a single character, so you can not have
##A


> 
> 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
> 
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-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,          75124 Uppsala, Sweden
phone:  46 18 471 4205          fax: 46 18 511 755
spoel at xray.bmc.uu.se    spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
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