[gmx-users] RNA woes
David van der Spoel
spoel at xray.bmc.uu.se
Thu Jul 21 09:12:05 CEST 2005
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
> 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
> 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
> As always, any and all help is dearly appreciated.
> Thanks in advance,
> 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
> 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)
> 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
> ATOM 102370 N LEU E 7 37.107 135.878 199.523
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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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