To generate starting (non-equilibrated) bilayer structures for use in MD
simulations take a look at http://www.ime.unicamp.br/~martinez/packmol/.
Otherwise, for conventional lipids CHARMM-GUI membrane builder
(http://www.charmm-gui.org/?doc=input/membrane).
Hope it helps!
Felipe
On
Dear Felipe,
thanks for advise. Does the Packmol software suitable for generation
coordinates of the bergers ( for gromos 56 ff) lipids ? As I know
CHARMM-GUI membrane builder is suitable for only CHARMM force field
lipids.
James
2012/10/4 Felipe Pineda, PhD luis.pinedadecas...@lnu.se:
To
Hi,
packmol generates just coordinates (pdb format) for optimized packing
arrangements of whatever molecule you provide as input. It's up to you
to parameterize the resulting model. CHARMM-GUI has a library of
conventional (phospho)lipids and generates the input for CHARMM
equilibration of
Hi James,
The bilayers from the CHARMM-GUI can be converted into any force field
using a simple script. For a united-atom force field you will need to
remove the non-polar hydrogens, rename the atoms and possibly reorder
some of the atoms in the lipids.
As for other methods to build
On 10/3/12 1:59 AM, James Starlight wrote:
Justin,
I've told about lower lipid density at the left and right edges of the
new system ( see new pic bellow with marked regions).
http://imageshack.us/photo/my-images/10/dppc.png/
I've started with system consisted of 118 lipids and 6000 water
Justin,
Might the modifications of the vdwradii.dat be suitable for such
system expanding or (on other hand) reduction (as in the below picture
are shown). In the lattter case I defined new box dimensions (smaller
than initial box dims) and would like to remove all side water-lipids
layer which
On 10/3/12 8:59 AM, James Starlight wrote:
Justin,
Might the modifications of the vdwradii.dat be suitable for such
system expanding or (on other hand) reduction (as in the below picture
are shown). In the lattter case I defined new box dimensions (smaller
than initial box dims) and would
Justin,
thanks for advises.
Finally how I could effectively reduce size of my system (in x and y )
to the defined pbc box size ( see picture to the previous comment) ?
I've noticed that increasing of x and y to the 12 nm I obtain ideal
shape of the bilayer without miss-matches of the left and
On 10/3/12 12:38 PM, James Starlight wrote:
Justin,
thanks for advises.
Finally how I could effectively reduce size of my system (in x and y )
to the defined pbc box size ( see picture to the previous comment) ?
I've noticed that increasing of x and y to the 12 nm I obtain ideal
shape of
Justin,
lastly, is there any other ways to obtain bilayers of desired
dimensions started from just one lipid oriented in desired way for
instance?
James
2012/10/3, Justin Lemkul jalem...@vt.edu:
On 10/3/12 12:38 PM, James Starlight wrote:
Justin,
thanks for advises.
Finally how I
Dear all!
Recently I've forced with the same problem as was in this topic :)
I have tieleman's lipids consisted of 128 dppc with water.
also I have system with the protein inserted in the same bilayer
I wounder to know
1- How I could change lipid number in the pure lipid bilayer (
increase up
On 10/2/12 2:16 PM, James Starlight wrote:
Dear all!
Recently I've forced with the same problem as was in this topic :)
I have tieleman's lipids consisted of 128 dppc with water.
also I have system with the protein inserted in the same bilayer
I wounder to know
1- How I could change lipid
Justin,
I've done exactly like you provide me ( changing only x and y )
but in that case the protein and the old lipids were slightly shifted
to one side of the new system. Is there any way to center the old
system in respect to the new solvent ?
Also I've noticed that when I increase size of
On 10/2/12 2:56 PM, James Starlight wrote:
Justin,
I've done exactly like you provide me ( changing only x and y )
but in that case the protein and the old lipids were slightly shifted
to one side of the new system. Is there any way to center the old
system in respect to the new solvent ?
Justin
Previously I've expanded initial system on Z-dim before the protein
was inserted to increase both water layers.
After current processing with Genbox there is no problems in Z
actually- it look likes sandwich with two broader bread layers and
narrower cutlet :) So the lipid layer in x and
On 10/2/12 3:49 PM, James Starlight wrote:
Justin
Previously I've expanded initial system on Z-dim before the protein
was inserted to increase both water layers.
After current processing with Genbox there is no problems in Z
actually- it look likes sandwich with two broader bread layers and
This is exactly what I've obtained
http://imageshack.us/photo/my-images/27/89293914.png/
the same effect was also in case of intact tieleman's lipid bilayers (
the water layers were broader than lipid after resizing with genbox)
James
2012/10/2, Justin Lemkul jalem...@vt.edu:
On 10/2/12
On 10/2/12 4:12 PM, James Starlight wrote:
This is exactly what I've obtained
http://imageshack.us/photo/my-images/27/89293914.png/
This looks completely normal. What I was asking for was an image of one of your
failed attempts that has whatever odd manifestation you've been trying to
Justin,
I've told about lower lipid density at the left and right edges of the
new system ( see new pic bellow with marked regions).
http://imageshack.us/photo/my-images/10/dppc.png/
I've started with system consisted of 118 lipids and 6000 water in dims 6x6x10
I've created new box with the
Dear all!
Recently I've forced with the opposite problem. I have pre-equilbrated
bilayer of highter dimensions than I need. How I could reduce lipid number
of such bilayer as well as reduce total dimensions of such system ?
E.g I have preequilibrated bilayer consisted of 340 lipids. I want to
On 6/11/12 6:05 AM, James Starlight wrote:
Dear all!
Recently I've forced with the opposite problem. I have pre-equilbrated bilayer
of highter dimensions than I need. How I could reduce lipid number of such
bilayer as well as reduce total dimensions of such system ?
E.g I have
Peter,
Thanks for advise.
I've found already pre-equilibrated POPC bilayers with 200 lipids. I've
examined that lipids and found that they are very similar to the berger's
lipids (it consists of equal nymber of atoms ) but the atom order in each
lipid is slightly different than in Tieleman's
Hi,
The easiest solution is probably to write a script that reorders the
structure file (gro for example, just swap the lines in each lipid, and
use editconf -f file.gro -resnr 1 to renumber) the way it is written
in the topology.
Cheers
Jon
On 2012-05-28 08:03, James Starlight wrote:
Either use genbox -cs popc128b.gro or genconf -f popc128b.gro -nbox x y 0
Tieleman's lipids require you to generate a dummy tpr for use with trjconv
to unwrap the pbc (trjconv -s em.tpr -f popc128b.pdb -o popc128b-nopbc.gro
-pbc mol -ur compact) first.
Lots of people have their own bilayer but
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