[gmx-users] RNA woes

Ken Rotondi ksr at chemistry.umass.edu
Thu Jul 21 17:41:08 CEST 2005 

On Jul 21, 2005, at 10:31 AM, David van der Spoel wrote:

> 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

I understand : )

>
>>
>> 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.

That's the chain identifier. See below for examples for chains A-G & O,  
P

>
>
>>
>> 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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>>
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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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