[gmx-users] RNA woes

Thu Jul 21 15:54:05 CEST 2005

Hello David (and all),

1) I only need to edit the xlateat.dat file and not the .rtp file?

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

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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