[gmx-users] RNA woes

David van der Spoel spoel at xray.bmc.uu.se
Thu Jul 21 16:31:23 CEST 2005 

On Thu, 2005-07-21 at 09:54 -0400, Ken Rotondi wrote:
> Hello David (and all),
> 
> 1) I only need to edit the xlateat.dat file and not the .rtp file?
it *should* be enough

> 
> 2) yes, there are chain identifiers A - P
> 
> 3) What I was trying to convey with ##A is that the .pdb file has  
> residue numbers with alphabetic modifiers, such as:
> 
> ATOM  37508  O3' URA A1142       2.882 221.994 284.334
> ATOM  37509  P   ADE A1142A      3.706 223.218 285.024
That looks weird,  the first A should not be there.


> 
> for Chain A residues 1142 and 1142A. I suspect that gromacs cannot  
> handle this and that I'll have to edit the .pdb file to have sequential  
> ordering of residues, not a problem (well, a little problem).
> 
> My biggest question is why gromacs thinks there are 4 chains when there  
> are clearly 16...
> 
> 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  96145  H2' ADE B 119      47.856 192.824 196.903
> TER
> ATOM  96146  N   GLY C   3     -19.144 208.081 341.656
> 
> ATOM  99289  OT2 LYS C 203     -22.338 199.866 326.683
> TER
> ATOM  99290  N   ILE D   9     114.526 221.775 305.427
> 
> 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
> 
> ATOM 105250  OT2 PHE E 180      17.811 139.952 211.183
> TER
> ATOM 105251  N   LEU F   7     -27.623 220.521 273.882
> 
> ATOM 107972  OT2 LYS F 179     -46.568 167.828 286.225
> TER
> ATOM 107973  N   PRO G   4     -10.109 165.344 331.322
> 
> etc.
> 
> ATOM 121485  OT2 VAL O  56      42.715 224.082 262.437
> TER
> ATOM 121486  N   HID P   4      33.296 182.714 330.149
> 
> HID is a histidine protonated at ND1 (HISA) (minor problem to change).  
> It makes its first appearance in chain C, so it's not the reason that  
> chains are being omitted.
> 
> Sorry about the length of these posts,
> 
> Ken
> 
> On Jul 21, 2005, at 3:12 AM, David van der Spoel wrote:
> 
> > 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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-- 
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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