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
--
==================================================
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
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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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send a mail to gmx-users-requ...@gromacs.org.
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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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