[gmx-users] Newbie: How to modify the topology file after adding ions?

[Tsjerk Wassenaar]

Hi Jose,

The references to NA+ and CL- have been changed, you can reload the
page in your browser if you care to continue. Now I still think your
statement was rather rude and showing disrespect to the time I put in
the tutorial. Apart from the reference to NA/CL you're also factually
incorrect in your statements. The first sentence of the second
paragraph under the heading 'Hands on ...' (top of the page) reads:

"""
This tutorial uses Gromacs (http://www.gromacs.org) version 4.5 and
most of the commands given are specific to this package.
"""

Later on that page, considering the addition of ions to the topology
there is the statement:

"""
Note the numbers of ions added, and verify that an excess of sodium
ions is added for neutralization. Having replaced a number of water
molecules with ions, the system topology in protein.top is not correct
anymore. Edit the topology file and decrease the number of solvent
molecules. Also add a line specifying the number of NA ions and a line
specifying the amount of CL.
"""

You may note I changed NA+ to NA and CL- to CL, but for the rest the
paragraph was not edited or added.

Although I feel personally addressed, I can add that you're not the
first to respond to the tutorial like this. It is common behaviour for
a subset of undergrad students that had to follow this course as part
of their curriculum. And the default answer is usually one of "read",
"read again" or "read better!".

Cheers,

Tsjerk


On Wed, Dec 7, 2011 at 8:29 PM, Jose Borreguero <borreguero at gmail.com> wrote:
> This tutorial doesn't seem to be quite useful, if so many errors pop up.
> Maybe it was implemented for Gromacs < 4.5.x but there's no info on the
> version it should be used.
>
> However, Lo and behold! I found that you have a nice page with Gromacs 4.5.x
> tutorials :D
> (http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/index.html)
> I'll give a try with the Lyzosyme one!
>
> - Jose
>
>
> On Wed, Dec 7, 2011 at 1:29 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:
>>
>>
>>
>> Jose Borreguero wrote:
>>>
>>> Hi Justin, thanks for your reply!
>>>
>>> I appended '-p protein.top' to genion. File protein.top was automatically
>>> updated by insertion of the following lines at the end of the file:
>>> /[ molecules ]
>>>
>>> ; Compound        #mols
>>> Protein_chain_A     1
>>> SOL         7791
>>> NA+         26
>>> CL-         23/
>>>
>>>
>>> My solvated PDB, protein-solvent.pdb contains lines like these:
>>> ATOM  24543  NA  NA+  8043      50.712  66.452  12.341  1.00  0.00
>>>
>>> Now when I run grommp, I get the error
>>> /Fatal error:
>>> No such moleculetype NA+/
>>>
>>>
>>> I checked file gromos45a3.ff/ions.itp. The sodium is included in this
>>> fashion:
>>> /[ moleculetype ]
>>>
>>> ; molname   nrexcl
>>> NA          1
>>> [ atoms ]
>>> ; id    at type res nr  residu name at name  cg nr  charge   mass
>>> 1       NA+     1       NA          NA             1        22.9898/
>>>
>>>
>>> It seems the naming convention of ions.itp is different than that of
>>> protein.top and protein-solvent.pdb. I changed protein.top and
>>
>>
>> What was your exact genion command?  If you tell genion to use "-pname
>> NA+" (which is wrong) you get this result.  Note that the error says the
>> moleculetype "NA+" is not found; the moleculetype name is "NA" instead.
>>
>>> protein-solvent.pdb to match the naming of ions.itp. Then when I run
>>> grompp I get the error:
>>> /ERROR 1 [file protein.top, line 7228]:
>>>
>>>  ERROR: One of the box lengths is smaller than twice the cut-off length.
>>>  Increase the box size or decrease rlist./
>>>
>>> The puzzling thing is that line 7228 of protein.top is the last line of
>>> the file, that is,
>>> CL      23
>>> So the error message is not much help :(
>>
>>
>> The problem comes from the coordinate file and settings of the .mdp file;
>> they are somehow incompatible such that they would cause a violation of the
>> minimum image convention.  Why the error points to the .top I cannot say.
>>
>>
>> -Justin
>>
>> --
>> ========================================
>>
>> 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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>
>
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-- 
Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
University of Groningen
The Netherlands