[gmx-users] single RNA nucleotide in CHARMM with phosphate problem with pdb2gmx

maria goranovic mariagoranovic at gmail.com
Wed Mar 23 10:10:27 CET 2011


Just an update, I decided to create a new residue for an isolated GMP. Well,
not really, because I used pdb2gmx to output a topology of a dimer, and then
modified it carefully to extract the topology of a phosphorylated GTP.

thank you !



On Tue, Mar 22, 2011 at 2:52 PM, maria goranovic
<mariagoranovic at gmail.com>wrote:

> the gro file was the input. I am attaching a pdb as well
>
> CRYST1    100.0    100.0    100.0  90.00  90.00  90.00 P 1           1
> ATOM      1  P   G   A   4       5.488  -0.842   0.708  1.00  0.00
>   P
> ATOM      2  OP1 G   A   4       6.418   0.258   1.047  1.00  0.00
>   O
> ATOM      3  OP2 G   A   4       5.367  -1.998   1.624  1.00  0.00
>   O
> ATOM      4  O5' G   A   4       4.010  -0.213   0.513  1.00  0.00
>   O
> ATOM      5  C5' G   A   4       3.816   1.098   0.014  1.00  0.00
>   C
> ATOM      6  C4' G   A   4       2.324   1.432  -0.121  1.00  0.00
>   C
> ATOM      7  O4' G   A   4       1.623   0.448  -0.862  1.00  0.00
>   O
> ATOM      8  C3' G   A   4       1.584   1.482   1.211  1.00  0.00
>   C
> ATOM      9  O3' G   A   4       1.869   2.669   1.934  1.00  0.00
>   O
> ATOM     10  C2' G   A   4       0.136   1.413   0.721  1.00  0.00
>   C
> ATOM     11  O2' G   A   4      -0.363   2.696   0.397  1.00  0.00
>   O
> ATOM     12  C1' G   A   4       0.241   0.597  -0.574  1.00  0.00
>   C
> ATOM     13  N9  G   A   4      -0.450  -0.705  -0.438  1.00  0.00
>   N
> ATOM     14  C8  G   A   4       0.075  -1.954  -0.237  1.00  0.00
>   C
> ATOM     15  N7  G   A   4      -0.808  -2.911  -0.197  1.00  0.00
>   N
> ATOM     16  C5  G   A   4      -2.017  -2.251  -0.377  1.00  0.00
>   C
> ATOM     17  C6  G   A   4      -3.346  -2.767  -0.450  1.00  0.00
>   C
> ATOM     18  O6  G   A   4      -3.705  -3.941  -0.398  1.00  0.00
>   O
> ATOM     19  N1  G   A   4      -4.299  -1.762  -0.593  1.00  0.00
>   N
> ATOM     20  C2  G   A   4      -4.002  -0.413  -0.682  1.00  0.00
>   C
> ATOM     21  N2  G   A   4      -5.023   0.438  -0.804  1.00  0.00
>   N
> ATOM     22  N3  G   A   4      -2.751   0.071  -0.652  1.00  0.00
>   N
> ATOM     23  C4  G   A   4      -1.809  -0.897  -0.499  1.00  0.00
>   C
> ATOM     24  H5' G   A   4       4.293   1.204  -0.960  1.00  0.00
>   H
> ATOM     25 H5'' G   A   4       4.269   1.819   0.696  1.00  0.00
>   H
> ATOM     26  H4' G   A   4       2.217   2.395  -0.623  1.00  0.00
>   H
> ATOM     27  H3' G   A   4       1.819   0.589   1.792  1.00  0.00
>   H
> ATOM     28  H2' G   A   4      -0.503   0.940   1.465  1.00  0.00
>   H
> ATOM     29 HO2' G   A   4      -1.301   2.614   0.210  1.00  0.00
>   H
> ATOM     30  H1' G   A   4      -0.225   1.145  -1.393  1.00  0.00
>   H
> ATOM     31  H8  G   A   4       1.129  -2.132  -0.139  1.00  0.00
>   H
> ATOM     32  H1  G   A   4      -5.265  -2.065  -0.635  1.00  0.00
>   H
> ATOM     33  H21 G   A   4      -5.974   0.099  -0.815  1.00  0.00
>   H
> ATOM     34  H22 G   A   4      -4.841   1.428  -0.876  1.00  0.00
>   H
> END
>
>
> On Tue, Mar 22, 2011 at 2:43 PM, Daniel Adriano Silva M <
> dadriano at gmail.com> wrote:
>
>> Hi,
>>
>> Is this your input? (a GRO file?). Can you paste the PDB corresponding to
>> the RNA nucleotide that you are interested on? I think the file may be small
>> enough to paste it here so someone can try to reproduce what is happening to
>> you.
>>
>> Daniel
>>
>>
>> 2011/3/22 maria goranovic <mariagoranovic at gmail.com>
>>
>>> Sorry for the incomplete reply.
>>> version 4.5.3,
>>> command: pdb2gmx -f guan.pdb -ignh
>>> I tried using -ter, but that did not help.
>>>
>>>
>>> input coordinate file, pulled out from an RNA molecule.
>>>
>>> Gromacs Runs On Most of All Computer Systems
>>>    34
>>>     1G        P    1   5.549   4.916   5.071
>>>     1G      OP1    2   5.642   5.026   5.105
>>>     1G      OP2    3   5.537   4.800   5.162
>>>     1G      O5'    4   5.401   4.979   5.051
>>>     1G      C5'    5   5.382   5.110   5.001
>>>     1G      C4'    6   5.232   5.143   4.988
>>>     1G      O4'    7   5.162   5.045   4.914
>>>     1G      C3'    8   5.158   5.148   5.121
>>>     1G      O3'    9   5.187   5.267   5.193
>>>     1G      C2'   10   5.014   5.141   5.072
>>>     1G      O2'   11   4.964   5.270   5.040
>>>     1G      C1'   12   5.024   5.060   4.943
>>>     1G       N9   13   4.955   4.930   4.956
>>>     1G       C8   14   5.008   4.805   4.976
>>>     1G       N7   15   4.919   4.709   4.980
>>>     1G       C5   16   4.798   4.775   4.962
>>>     1G       C6   17   4.665   4.723   4.955
>>>     1G       O6   18   4.630   4.606   4.960
>>>     1G       N1   19   4.570   4.824   4.941
>>>      1G       C2   20   4.600   4.959   4.932
>>>     1G       N2   21   4.498   5.044   4.920
>>>     1G       N3   22   4.725   5.007   4.935
>>>     1G       C4   23   4.819   4.910   4.950
>>>     1G      H5'   24   5.429   5.120   4.904
>>>     1G     H5''   25   5.427   5.182   5.070
>>>     1G      H4'   26   5.222   5.240   4.938
>>>     1G      H3'   27   5.182   5.059   5.179
>>>     1G      H2'   28   4.950   5.094   5.146
>>>     1G     HO2'   29   4.870   5.261   5.021
>>>     1G      H1'   30   4.978   5.115   4.861
>>>     1G       H8   31   5.113   4.787   4.986
>>>     1G       H1   32   4.474   4.794   4.936
>>>     1G      H21   33   4.403   5.010   4.918
>>>     1G      H22   34   4.516   5.143   4.912
>>>   10.00000  10.00000  10.00000
>>>
>>>
>>> On Tue, Mar 22, 2011 at 2:09 PM, Mark Abraham <Mark.Abraham at anu.edu.au>wrote:
>>>
>>>>  On 22/03/2011 8:15 PM, maria goranovic wrote:
>>>>
>>>> is this a bug of some kind then? someone ? anyone?
>>>>
>>>>
>>>> It's still hard to say. I asked you for your GROMACS version and input
>>>> coordinate file, and you didn't give us either (in full). While you're
>>>> there, what pdb2gmx command did you use?
>>>>
>>>> Mark
>>>>
>>>>
>>>>  just bumping,
>>>>
>>>>  maria
>>>>
>>>> On Mon, Mar 21, 2011 at 10:17 AM, maria goranovic <
>>>> mariagoranovic at gmail.com> wrote:
>>>>
>>>>> Here are the contents of my input coordinate file.
>>>>>
>>>>>  CRYST1    0.000    0.000    0.000  90.00  90.00  90.00 P 1
>>>>> 1
>>>>> ATOM      1  P   G   A   4       5.488  -0.842   0.708  1.00  0.00
>>>>>       P
>>>>> ATOM      2  OP1 G   A   4       6.418   0.258   1.047  1.00  0.00
>>>>>       O
>>>>> ATOM      3  OP2 G   A   4       5.367  -1.998   1.624  1.00  0.00
>>>>>       O
>>>>> ATOM      4  O5' G   A   4       4.010  -0.213   0.513  1.00  0.00
>>>>>       O
>>>>> ATOM      5  C5' G   A   4       3.816   1.098   0.014  1.00  0.00
>>>>>       C
>>>>> ATOM      6  C4' G   A   4       2.324   1.432  -0.121  1.00  0.00
>>>>>       C
>>>>> ATOM      7  O4' G   A   4       1.623   0.448  -0.862  1.00  0.00
>>>>>       O
>>>>> ATOM      8  C3' G   A   4       1.584   1.482   1.211  1.00  0.00
>>>>>       C
>>>>> ....
>>>>> ATOM     33  H21 G   A   4      -5.974   0.099  -0.815  1.00  0.00
>>>>>       H
>>>>> ATOM     34  H22 G   A   4      -4.841   1.428  -0.876  1.00  0.00
>>>>>       H
>>>>>
>>>>>
>>>>>    Of course it would be best if pdb2gmx worked as it is if I just
>>>>> have a single nucleotide, and not a chain?
>>>>>
>>>>>
>>>>>  Here, I am wondering if the above problem is occurring because
>>>>> pdb2gmx is not being able to deal with an isolated nucleotide (while it
>>>>> might be able to deal with an polymer)
>>>>>
>>>>>  Maria
>>>>>
>>>>>
>>>>>  On Sat, Mar 19, 2011 at 5:44 AM, Mark Abraham <
>>>>> mark.abraham at anu.edu.au> wrote:
>>>>>
>>>>>>
>>>>>>
>>>>>> On 19/03/11, *maria goranovic * <mariagoranovic at gmail.com> wrote:
>>>>>>
>>>>>> Dear All
>>>>>>
>>>>>>  I am trying to generate a topology for guanosine monophosphate: i.e.
>>>>>> an RNA base with a phosphate at the 5' Carbon. I tried to read in a pdb file
>>>>>> containing all atoms, and used pdb2gmx with CHARMM. However, the output
>>>>>> coordinate file has no phosphate group on it. Why does the phosphate
>>>>>> disappear, and why does pdb2gmx not even give me a warning?
>>>>>>
>>>>>>
>>>>>>  That does sound suspicious, but it's hard to say what went wrong.
>>>>>> What GROMACS version was it, and what were the contents of your input
>>>>>> coordinate file?
>>>>>>
>>>>>>
>>>>>>  Assuming that a molecule like GMP does not have a topology, I am
>>>>>> guessing I might have to make a new residue within CHARMM. that should not
>>>>>> be too much work because there is no new angle/dihedral/bond/atom type to be
>>>>>> be added. Can someone please help me with a simple workflow so I do not miss
>>>>>> something important?
>>>>>>
>>>>>>
>>>>>>  The procedure is outlined here:
>>>>>> http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_FieldYour case should be a reasonably straightforward exercise in assigning
>>>>>> sensible atom types from the pre-existing options.
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>> Mark
>>>>>> --
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>>>>>>
>>>>>
>>>>>
>>>>>
>>>>> --
>>>>> Maria G.
>>>>> Technical University of Denmark
>>>>> Copenhagen
>>>>>
>>>>
>>>>
>>>>
>>>> --
>>>> Maria G.
>>>> Technical University of Denmark
>>>> Copenhagen
>>>>
>>>>
>>>>
>>>> --
>>>> gmx-users mailing list    gmx-users at gromacs.org
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>>>
>>>
>>>
>>> --
>>> Maria G.
>>> Technical University of Denmark
>>> Copenhagen
>>>
>>> --
>>> gmx-users mailing list    gmx-users at gromacs.org
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>>
>>
>> --
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>
>
>
> --
> Maria G.
> Technical University of Denmark
> Copenhagen
>



-- 
Maria G.
Technical University of Denmark
Copenhagen
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