Hi Justin, Thanks for that information.
I also would like to confirm with you that should I combine my metal ion too
while I combine Protein and POPC into Protein_POPC group to be used in COMM
removal? So that I will have a group Protein_HEM_POPC.
Thanks
Peterson J
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On 7/27/12 8:50 AM, J Peterson wrote:
Hi Justin, Thanks for that information.
I also would like to confirm with you that should I combine my metal ion too
while I combine Protein and POPC into Protein_POPC group to be used in COMM
removal? So that I will have a group Protein_HEM_POPC.
With
Thanks for that comment.
I've another query during inflating step in Justin's tutorial.
In my case, during the inflation, 4 lipids from the upper and 2 lipids from
the lower leaflets were removed.
Would there be a problem in this sort non-uniform deletion (I mean like 4
from upper and 4 from
On 7/24/12 2:49 AM, J Peterson wrote:
Thanks for that comment.
I've another query during inflating step in Justin's tutorial.
In my case, during the inflation, 4 lipids from the upper and 2 lipids from
the lower leaflets were removed.
Would there be a problem in this sort non-uniform
Hi Justin,
Thanks for all your help to get me through membrane simulations.
I've a problem to be solved. I need a long and thick membrane to simulate a
big protein. The longest bilayer that I can download from Tieleman's website
is 64 molecules long.
How can I make (double or triple the
On 7/23/12 5:31 AM, J Peterson wrote:
Hi Justin,
Thanks for all your help to get me through membrane simulations.
I've a problem to be solved. I need a long and thick membrane to simulate a
big protein. The longest bilayer that I can download from Tieleman's website
is 64 molecules long.
Thank you so much for that, Justin.
Now I could expand the bilayer.
I've another query. My protein has a small N-terminal portion embedded in
the membrane, I would like to insert only this part into the membrane during
'packing the lipid around the protein' step in your tutorial. Initially I
On 7/23/12 7:53 AM, J Peterson wrote:
Thank you so much for that, Justin.
Now I could expand the bilayer.
I've another query. My protein has a small N-terminal portion embedded in
the membrane, I would like to insert only this part into the membrane during
'packing the lipid around the
Hi Justin,
That works really fine and thanks.
Now, how can I add additional SOL molecules only one side of the bilayer
(either upper or lower)? Since my protein binds at the outer side
(extracellular region) of the membrane I can only fill the upper
(extracellular) region with SOL molecules
On 24/07/2012 2:57 PM, J Peterson wrote:
Hi Justin,
That works really fine and thanks.
Now, how can I add additional SOL molecules only one side of the bilayer
(either upper or lower)? Since my protein binds at the outer side
(extracellular region) of the membrane I can only fill the upper
Hi Justin,
I have the following Notes during NPT equilibration.
NOTE 1 [file pr_NPT.mdp]:
nstcomm nstcalcenergy defeats the purpose of nstcalcenergy, setting
nstcomm to nstcalcenergy
NOTE 2 [file pr_NPT.mdp]:
leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
On 7/17/12 4:05 AM, J Peterson wrote:
Hi Justin,
I have the following Notes during NPT equilibration.
NOTE 1 [file pr_NPT.mdp]:
nstcomm nstcalcenergy defeats the purpose of nstcalcenergy, setting
nstcomm to nstcalcenergy
http://manual.gromacs.org/online/mdp_opt.html#out
I have the following Notes during NPT equilibration.
NOTE 1 [file pr_NPT.mdp]:
nstcomm nstcalcenergy defeats the purpose of nstcalcenergy, setting
nstcomm to nstcalcenergy
NOTE 2 [file pr_NPT.mdp]:
leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
What do
Hi Justin,
I have another doubt on the strong posres that was included in the topology
file. When do we need to remove that position restraint? Does it really
affect at point of time the system?
Thanks
Peterson J
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On 7/13/12 1:44 AM, J Peterson wrote:
Thanks for the comment. By the way how to make a bigger box at this time of
the tutorial without affecting any part of the system. Can I use editconf
with slightly bigger number for z-axis (something like 6.7 which was 5.7
before)?
The box should be
On 7/13/12 4:14 AM, J Peterson wrote:
Hi Justin,
I have another doubt on the strong posres that was included in the topology
file. When do we need to remove that position restraint? Does it really
affect at point of time the system?
The strong restraints are only needed for InflateGRO.
Thanks Justin,
The explanations are very very useful during my course of simulating a
protein with POPC.
I also would like to get explanation on how to simulate a protein which has
only its N-terminal region embedded in the membrane but the rest in solvent.
What is the easy and accurate way to
On 7/13/12 6:44 AM, J Peterson wrote:
Thanks Justin,
The explanations are very very useful during my course of simulating a
protein with POPC.
I also would like to get explanation on how to simulate a protein which has
only its N-terminal region embedded in the membrane but the rest in
Hi Justin,
Thanks for the effort to help me.
I still no out of the error. The following is the content of my
topol_popc.top
; Include chain topologies
#include gromos53a6_lipid.ff/forcefield.itp
#include popc.itp
; Include water topology
#include gromos53a6_lipid.ff/spc.itp
; Include ion
On 7/12/12 4:59 AM, J Peterson wrote:
Hi Justin,
Thanks for the effort to help me.
I still no out of the error. The following is the content of my
topol_popc.top
; Include chain topologies
#include gromos53a6_lipid.ff/forcefield.itp
#include popc.itp
; Include water topology
#include
Hi Justin,
Thanks for the suggestion I got it solved somehow. The main problem was in
the popc128b.pdb itself, it has first 64 lipids and half of the SOl
molecules followed by rest of the POPC and SOL molecules. When I rearranged
them the error was solved.
But now another thing I would like to
On 7/12/12 10:23 PM, J Peterson wrote:
Hi Justin,
Thanks for the suggestion I got it solved somehow. The main problem was in
the popc128b.pdb itself, it has first 64 lipids and half of the SOl
molecules followed by rest of the POPC and SOL molecules. When I rearranged
them the error was
Hi Justin,
I followed your comments and now at the stage of adding solvents.
I wonder to see the protein after shrinking step to have no SOL molecules as
there were SOL molecules in the source popc128b.pdb. Had we removed all the
original SOL molecules anywhere during the course of tutorial?
I
On 7/13/12 12:24 AM, J Peterson wrote:
Hi Justin,
I followed your comments and now at the stage of adding solvents.
I wonder to see the protein after shrinking step to have no SOL molecules as
there were SOL molecules in the source popc128b.pdb. Had we removed all the
original SOL molecules
Thanks for the comment. By the way how to make a bigger box at this time of
the tutorial without affecting any part of the system. Can I use editconf
with slightly bigger number for z-axis (something like 6.7 which was 5.7
before)?
Thanks
Peterson J
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