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.
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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.abra...@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 <
> mariagorano...@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.abra...@anu.edu.au>wrote:
>>
>>>
>>>
>>> On 19/03/11, *maria goranovic * <mariagorano...@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@gromacs.org
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>>>
>>
>>
>>
>> --
>> Maria G.
>> Technical University of Denmark
>> Copenhagen
>>
>
>
>
> --
> Maria G.
> Technical University of Denmark
> Copenhagen
>
>
>
> --
> gmx-users mailing list gmx-users@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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