[gmx-users] single RNA nucleotide in CHARMM with phosphate problem with pdb2gmx
maria goranovic
mariagoranovic at gmail.com
Tue Mar 22 14:52:29 CET 2011
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
>>>>> --
>>>>> gmx-users mailing list gmx-users at gromacs.org
>>>>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>>>>> Please search the archive at
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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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>>> Please search the archive at
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>>
>>
>>
>> --
>> Maria G.
>> Technical University of Denmark
>> Copenhagen
>>
>> --
>> gmx-users mailing list gmx-users at gromacs.org
>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>> Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
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>
>
> --
> gmx-users mailing list gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
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--
Maria G.
Technical University of Denmark
Copenhagen
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