[gmx-users] single RNA nucleotide in CHARMM with phosphate problem with pdb2gmx
Daniel Adriano Silva M
dadriano at gmail.com
Tue Mar 22 14:43:19 CET 2011
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
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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
>> 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
>
> --
> 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!
> Please don't post (un)subscribe requests to the list. Use the
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