[gmx-users] genconf to insert small molecules triclinic unit cell
Justin A. Lemkul
jalemkul at vt.edu
Fri Oct 22 15:51:49 CEST 2010
Jennifer Williams wrote:
>
> Hi Justin,
>
> The .pdb I sent with my last e-mail was a result of trying to add 500
> molecules. The max of 168 were added and then genconf couldn't add
> anymore despite the large vacant space. Trying to add more molecules to
> this .pdb won't work. This is what makes me think the space was somehow
> inaccessible.
>
OK, my previous comments had assumed that you were trying to insert 100
molecules, per your first post. Inserting 500 is another matter. It looks like
genbox is trying to build a cubic configuration that intersects your triclinic
cell. Very weird. Your cell may not be large enough for 500 molecules, given
the constraints of VDW distances, but you certainly shouldn't have any voids.
You may be able to generate a box of NO molecules and try to use these molecules
as a "solvent" of sorts, using -cs.
> If I carry out an mdrun on this structure, the NO molecules distribute
> themselves into this empty space. If I take the structure file following
> MD I can add an extra 24 molecules with genbox.
>
> The worry is not for these small NO molecules where I can use MD to
> create more space. I am also trying to insert larger organic molecules
> and if parts of the unit cell are seen as inaccessible I won't be able
> to get the molecules in there in the first place.
>
My suspicion is that the box is somehow not being processed correctly when
molecules are inserted, but I can't really back that up with any hard evidence,
other than that's what it looks like in VMD :)
Maybe someone else will have some insight.
-Justin
>
> Jenny
>
>
>
>
> Quoting "Justin A. Lemkul" <jalemkul at vt.edu>:
>
>>
>>
>> Jennifer Williams wrote:
>>>
>>> Hi Justin,
>>>
>>> Thanks for the response (again!).
>>>
>>> I would be happy if genbox inserted molecules randomly (within the
>>> box defined by my .pdf file) but the output doesn't look random but
>>> subject to some strange (symmetry?)constraints which don't allow
>>> random insertions into some areas of my unit cell.
>>>
>>> The molecules will crowd into one space leaving another portion of
>>> the cell completely empty. The inserted molecules assume the shape
>>> of a box whilst the rest of my structure is a triclinic cell.
>>>
>>> One pic is probably worth a thousand words. I've attached a .pdb of
>>> the final structure. I'd appreciate if you could tell me if this is
>>> normal output for genbox,
>>>
>>
>> I see nothing wrong with it. Looks like genbox started adding
>> molecules on one "side" of your box, and continued adding until it
>> reached 100, then stopped. Looks like you simply have more than enough
>> space to add more of your NO molecules, that's all. The molecules are
>> all within the unit cell, so I see no issue.
>>
>> If you want a more homogeneous distribution of NO, you may have to come
>> up with a different method.
>>
>> -Justin
>>
>>> Thanks very much
>>>
>>> Jenny
>>>
>>>
>>>
>>>
>>> Quoting "Justin A. Lemkul" <jalemkul at vt.edu>:
>>>
>>>>
>>>>
>>>> Jennifer Williams wrote:
>>>>> Hi,
>>>>>
>>>>> I have a strange problem when I try to insert small molecules
>>>>> into my cell using genconf. Here the cell is a crystalline
>>>>> metal-organic framework with lots of space for the molecules
>>>>> inside. The edges of the metal organic framework defined the pbcs.
>>>>>
>>>>> When I view the final structure, the inserted molecules appear to
>>>>> have a different symmetry to that of the MOF/cell. They notieably
>>>>> avoid some empty regions inside the box and are inserted outside
>>>>> regions of my triclinic cell. The inserted molecules don?t occupy
>>>>> a triclinic shape at all.
>>>>>
>>>>> I have used this feature before on a similar triclinic cell and
>>>>> it worked perfectly. I can?t tell what I am doing wrong this time.
>>>>>
>>>>> I outline the steps I take below.
>>>>>
>>>>> 1. I am trying to insert a number of molecules of NO into a
>>>>> triclinic crystal cell. The pdb file of the crystal cell has the
>>>>> following cell parameters.
>>>>>
>>>>> CRYST1 25.885 25.885 6.806 90.00 90.00 120.00 P 1 1
>>>>>
>>>>> This is the pdb file of the small molecule I am trying to insert:
>>>>>
>>>>> CRYST1 25.885 25.885 27.2232 90.00 90.00 120.00 P
>>>>> 1 1
>>>>> HETATM 1 NNO NOO 1 1.150 0.000 0.000 1.00 0.00
>>>>> N
>>>>> HETATM 2 ONO NOO 1 0.000 0.000 0.000 1.00 0.00
>>>>> O
>>>>> CONECT 1 2
>>>>> END
>>>>>
>>>>> I use the following commands:
>>>>>
>>>>> To centre the cell:
>>>>> editconf -c -f MOF.pdb -o MOF_centered.pdb
>>>>>
>>>>> To make a 1x1x4 box ( I need to increase the length in z) so that
>>>>> I can use sensible cut-offs later on
>>>>>
>>>>> genconf -nbox 1 1 4 -f MOF_centered.pdb -o MOF_4c.pdb
>>>>>
>>>>>
>>>>> To add the NO molecules:
>>>>>
>>>>> genbox ?cp MOF_4c.pdb -ci NOO.pdb -nmol 100 -o inserted_NO.pdb
>>>>>
>>>>> Any ideas appreciated as I have been going around in circles.
>>>>>
>>>>>
>>>>
>>>> When using genbox -ci, there is no guarantee of any type of symmetry.
>>>> It inserts molecules randomly, wherever it finds space. I don't think
>>>> you're doing anything wrong, I think you're just encountering a
>>>> limitation of genbox.
>>>>
>>>> -Justin
>>>>
>>>>> I am using gromacs 4.0.7
>>>>>
>>>>> Thanks
>>>>>
>>>>> Jenny
>>>>>
>>>>>
>>>>
>>>> --
>>>> ========================================
>>>>
>>>> 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
>>>>
>>>> ========================================
>>>> --
>>>> gmx-users mailing list gmx-users at gromacs.org
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>>>
>>>
>>>
>>>
>>>
>>
>> --
>> ========================================
>>
>> 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
>>
>> ========================================
>> --
>> 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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>
>
>
> Dr. Jennifer Williams
> Institute for Materials and Processes
> School of Engineering
> University of Edinburgh
> Sanderson Building
> The King's Buildings
> Mayfield Road
> Edinburgh, EH9 3JL, United Kingdom
> Phone: ++44 (0)131 650 4 861
>
>
--
========================================
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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