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.
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.
Jenny
Quoting "Justin A. Lemkul" <jalem...@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" <jalem...@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@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 www
interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
--
========================================
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@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 www
interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
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
--
The University of Edinburgh is a charitable body, registered in
Scotland, with registration number SC005336.
--
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!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
