[gmx-users] single RNA nucleotide in CHARMM with phosphate problem with pdb2gmx
Justin A. Lemkul
jalemkul at vt.edu
Tue Mar 22 14:43:49 CET 2011
maria goranovic wrote:
> Sorry for the incomplete reply.
> version 4.5.3,
> command: pdb2gmx -f guan.pdb -ignh
> I tried using -ter, but that did not help.
>
>
It appears that pdb2gmx is not equipped to handle the case of an isolated
nucleotide. Keep in mind that pdb2gmx is intended for use with repeat building
blocks of monomers, not isolated molecules. The default behavior is to assign a
5' end with no phosphate (i.e. RG rather than pRG). Attempting to choose "None"
for a terminus leaves an incomplete phosphate group (i.e. PO3 instead of PO4)
and thus a fatal error about a "dangling bond." I'm guessing this has been your
experience?
There are two potential solutions:
1. Write an .rtp entry of a complete, custom RG nucleotide with the desired PO4
5' end.
2. Write a new entry in rna.n.tdb that adds another phosphate oxygen and adjusts
charges appropriately by replacing the existing O and P atoms, at least.
-Justin
> 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
> <mailto: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 <mailto: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 <mailto:mark.abraham at anu.edu.au>> wrote:
>>
>>
>>
>> On 19/03/11, *maria goranovic * <mariagoranovic at gmail.com
>> <mailto: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_Field
>> Your 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
>
>
> --
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>
>
> --
> Maria G.
> Technical University of Denmark
> Copenhagen
>
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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