On 7/15/16 3:16 PM, roshanak starlight wrote:
1.in end of topology file , i have sol.it dosen't water?should i remove
that?
Again, topol_dppc.top has absolutely nothing to do with the topol.top that
should be used for the protein-membrane system. Ignore it once you have made
the DPPC whole. There is no water in the output configuration of InflateGRO, by
design (the paper regarding this method explains why). If you were to add
water, you would have a half million atom system that would probably never
minimize to anything sensible, as well as distorting your lipids. Follow the
tutorial exactly and do not confuse file names.
2.minim.mdp file is not exist for this step
Yes it does. It is linked from the step 3 page.
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/Files/minim.mdp
-Justin
On Jul 15, 2016 8:49 PM, "Justin Lemkul" <jalem...@vt.edu> wrote:
On 7/15/16 12:15 PM, roshanak starlight wrote:
thank you for answers
after this command :grompp -f minim.mdp -c system_inflated.gro -p
topol.top
-o em.tpr
i receive 2 note :
NOTE 1 [file topol.top, line 927]:
System has non-zero total charge: 4.000000
Total charge should normally be an integer.
should i add ion ? with ion.itp that is in gromos53a6_lipid.ff ?
No, because there is no water (nor should there be).
NOTE 2 [file minim.mdp]:
The optimal PME mesh load for parallel simulations is below 0.5
and for highly parallel simulations between 0.25 and 0.33,
for higher performance, increase the cut-off and the PME grid spacing
.what is it's reason and what should i do ?.i used from same minim.mdp
file
that was for dppc( in tutorial.)
should i change cut off ?on what basis? i don't find it in manual
Use the files from the tutorial. Performance during EM is not anything of
major importance. There's no way to take a huge, inflated system in vacuo
and make it very efficient.
-Justin
On Fri, Jul 15, 2016 at 6:27 PM, Justin Lemkul <jalem...@vt.edu> wrote:
On 7/15/16 9:55 AM, roshanak starlight wrote:
excuse me.i don't understand . should i update [molecule] just in
*topol.top* ? how?
my topol.top file in [molecule] has not any number :
[ molecules ]
; Compound #mols
Protein 1
Add a line that says "DPPC 126"
You have to manually account for changes that are being made to the
coordinate file. Please do some more basic tutorial material if the
content and organization of a topology is unfamiliar to you.
-Justin
in my topol_dppc.top is this:
[ molecules ]
; molecule name nr.
DPPC 128
SOL 3655
On Fri, Jul 15, 2016 at 6:12 PM, Justin Lemkul <jalem...@vt.edu> wrote:
On 7/15/16 9:40 AM, roshanak starlight wrote:
should i do this ? :
i should change dppc from 128lipid (topol_dppc.top) to 6300atom and
topol_dppc.top is only ever used for making molecules whole, and never
again.
system_inflated.gro from 6348 t0 6300 ?
Do not change the .gro file at all.
but why is number of system.gro 6538 ? (6400 + 138)
In system.gro (and the corresponding topol.top) you have 128 lipids
and
the peptide. Then InflateGRO removes two of those lipids, so you have
to
account for this in topol.top, which now has the peptide and 126
lipids.
-Justin
50 is atom per lipid
On Fri, Jul 15, 2016 at 5:58 PM, Justin Lemkul <jalem...@vt.edu>
wrote:
On 7/15/16 9:26 AM, roshanak starlight wrote:
hello . when i want to do energy minimizationin step 3 , with this
command: grompp -f minim.mdp -c system_inflated.gro -p topol.top -o
em.tpr
(or confout.gro replace em.tpr) i face with this error:
Fatal error:
number of coordinates in coordinate file (system_inflated.gro, 6438)
does not match topology (topol.top, 138)
Earlier, right after this command : perl inflategro.pl system.gro 4
DPPC
14
system_inflated.gro 5 area.dat
, i updated [molecules] in topol-dppc.top from 128 to 126 dppc
(because
of
this sentence in terminal:
There are 2 lipids within cut-off range...
1 will be removed from the upper leaflet...
1 will be removed from the lower leaflet...)
where is the problem from ?
Apparently you didn't actually update the topology.
126 * 50 = 6300
6438 - 138 = 6300
So your topology specifies no lipids.
-Justin
On Fri, Jul 15, 2016 at 2:16 PM, Justin Lemkul <jalem...@vt.edu>
wrote:
On 7/15/16 4:56 AM, roshanak starlight wrote:
excuse me i forgot that write subject.
On Fri, Jul 15, 2016 at 1:20 PM, roshanak starlight <
starlight....@gmail.com
wrote:
hello
i use kalp-15 in dppc tutorial that there is in this website :
http://www.bevanlab.biochem.vt.edu
i have 2 question about step 3 :
1.after this command : genrestr -f KALP_newbox.gro -o
strong_posre.itp
-fc 100000 100000 100000 which shoud i choose ? ( i choose
1:protein .
is it right ?)
From the tutorial:
"The authors of the InflateGRO script recommend using a very
strong
position-restraining force on protein heavy atoms to ensure that
the
position of the protein does not change during EM."
So choose the protein heavy atoms (Protein-H).
2.where should i add a line "define = -DSTRONG_POSRES" in
minim.mdp
?
i
add it (define = -DSTRONG_POSRES ) to end of my file . is it true?
thank you
It doesn't matter.
-Justin
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Ruth L. Kirschstein NRSA Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul
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Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul
==================================================
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Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul
==================================================
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Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul
==================================================
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==================================================
Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul
==================================================
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