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<div class="moz-cite-prefix">On 20/06/2012 4:39 PM, James Starlight
wrote:<br>
</div>
<blockquote
cite="mid:CAALQopyLogvbwXf-F_+JkH+mNO3f7Pv3o_-y_j5b_4DQRT+H3Q@mail.gmail.com"
type="cite">by the way I've forced with problems during insertion
of the complex protein_ligand into membrane by means of g_membed<br>
<br>
firstly I've created index.ndx file with the merged protein_ligand
group. Than I've used next mdp for my g_membed input<br>
<br>
integrator = md<br>
energygrps = Protein ADN<br>
freezegrps = Protein ADN<br>
freezedim = Y Y Y<br>
energygrp_table<br>
energygrp_excl = Protein Protein<br>
<br>
here ADN is the ligand<br>
<br>
than I've tried to generate input file for g_membed where I've
selected my protein_ligand group to be inserted into membrane but
I've obtained this eror althought protein_ligand group were
presented in the list of aviable groups for insertion<br>
<br>
Fatal error:<br>
Group Protein_ADN not found in indexfile.<br>
Maybe you have non-default groups in your mdp file, while not
using the '-n' option of grompp.<br>
In that case use the '-n' option.<br>
</blockquote>
<br>
So clearly you haven't given grompp an index file with the merged
protein-and-ligand group that matches the .mdp file usage. Since
you're changing nomenclature at least once in the course of this
email, that's not surprising. You may not have the patience to check
your spelling in email, but grompp will insist on everything to its
satisfaction...<br>
<br>
Mark<br>
<br>
<blockquote
cite="mid:CAALQopyLogvbwXf-F_+JkH+mNO3f7Pv3o_-y_j5b_4DQRT+H3Q@mail.gmail.com"
type="cite"><br>
Finally If I've tried to insert kust protein intoi membrane than
G_membed delete my ligand during insertion<br>
<br>
Will remove 0 Protein molecules<br>
Will remove 1 ADN molecules<br>
Will remove 10 POP molecules<br>
Will remove 41 SOL molecules<br>
<br>
How I could fix this problem and obtain whole protein_ligand
system inserted in the membrane ?<br>
<br>
<br>
James<br>
<br>
<br>
<div class="gmail_quote">2012/6/15 James Starlight <span
dir="ltr"><<a moz-do-not-send="true"
href="mailto:jmsstarlight@gmail.com" target="_blank">jmsstarlight@gmail.com</a>></span><br>
<blockquote class="gmail_quote" style="margin:0 0 0
.8ex;border-left:1px #ccc solid;padding-left:1ex">
I've found main reason of such crushes. It was due to the
individual internal waters wich I've included to my model as
the buried to the protein interiour ( the coordinates were
copppied form X-ray structure of the same protein). <br>
<br>
By the way I have already performed the same simulation with
the inclussion of the same X-ray waters but in different
system with membrane-mimicking env. consisted of Ccl4 in
water. As the result there have not been any problems with
that system.<br>
<br>
Finally I have some question about G_membed acceleration.
I've noticed that the process of insertion of the protein in
the membrane is very long (actually it's only 50ps
simulation).<br>
<br>
During procesing of my system I've obtained notes like<br>
<br>
NOTE 4 [file topol.top, line 19511]:<br>
For energy conservation with LINCS, lincs_iter should be 2
or larger.<br>
<br>
NOTE 1 [file gmembed.mdp]:<br>
You are using a cut-off for VdW interactions with NVE, for
good energy<br>
conservation use vdwtype = Shift (possibly with DispCorr)<br>
<br>
NOTE 2 [file gmembed.mdp]:<br>
You are using a cut-off for electrostatics with NVE, for
good energy<br>
conservation use coulombtype = PME-Switch or
Reaction-Field-zero<br>
<br>
The parameters for long-range and short-range interactions
I've used from my typical simulation on the lipid Gromos56-ff
( presented in the Justin's tutorial).<br>
<br>
Is there any other parameters for that object wich are most
suitable for G_membed ?<span class="HOEnZb"><font
color="#888888"><br>
<br>
James</font></span>
<div class="HOEnZb">
<div class="h5"><br>
<br>
<br>
<div class="gmail_quote">2012/6/14 James Starlight <span
dir="ltr"><<a moz-do-not-send="true"
href="mailto:jmsstarlight@gmail.com" target="_blank">jmsstarlight@gmail.com</a>></span><br>
<blockquote class="gmail_quote" style="margin:0 0 0
.8ex;border-left:1px #ccc solid;padding-left:1ex">
Mark,<br>
<br>
I've used commands provided in the G_membed manual<br>
<br>
g membed -f input.tpr -p merged.top -xyinit 0.1
-xyend 1.0 -nxy 1000 <br>
<br>
or<br>
<br>
g membed -f input.tpr -p merged.top -xyinit 0.1
-xyend 1.0 -nxy 1000 -zinit 1.1 -zend 1.0 -nz 100<br>
<br>
<br>
In both cases I've obtained the same message<br>
<br>
There are 122 lipids in the membrane part that
overlaps the protein.<br>
The area per lipid is 0.5002 nm^2.<br>
Maximum number of lipids that will be removed is 45.<br>
<br>
and eventually only 10 lipids were removed. Also I've
tried to do this on another pope bilayer (consisted of
bigger lipids with properly equilirated ) but I've
obtained exactly the same results.<br>
<br>
<br>
James<br>
<br>
<div class="gmail_quote">2012/6/14 Mark Abraham <span
dir="ltr"><<a moz-do-not-send="true"
href="mailto:Mark.Abraham@anu.edu.au"
target="_blank">Mark.Abraham@anu.edu.au</a>></span><br>
<blockquote class="gmail_quote" style="margin:0 0 0
.8ex;border-left:1px #ccc solid;padding-left:1ex">
<div>
<div>
<div bgcolor="#FFFFFF" text="#000000">
<div> On 14/06/2012 4:39 PM, James Starlight
wrote:
<blockquote type="cite">Dear Gromacs
Users!<br>
<br>
I've forced with the problem durin
insertion of my protein into
pre-equilibrated bilayer via G_Membed. <br>
<br>
I've done all steps in accordance to the
KALP tutorial ( I've oriented both
membrane as well as the protein in the
same dimensions merged both topologies
and gro files in the merged.gro file )
but after processed via grompp I've
recieved warning<br>
<br>
WARNING 1 [file gmembed.mdp]:<br>
Can not exclude the lattice Coulomb
energy between energy groups<br>
</blockquote>
<br>
</div>
You've asked about this before... <a
moz-do-not-send="true"
href="http://lists.gromacs.org/pipermail/gmx-users/2011-November/066002.html"
target="_blank">http://lists.gromacs.org/pipermail/gmx-users/2011-November/066002.html</a>
<div>
<br>
<br>
<blockquote type="cite">if I scip this
message by maxwarn oprtins, g_membed
remove only 10 lipids ( while > 40
are overlapped with the protein ) and
during further g_membed's md_run I've
obtained lincs warning and my system is
crushed .<br>
</blockquote>
<br>
</div>
Have you followed g_membed -h and their
published method? You've not shown your
command lines, so it's impossible for anyone
to know what you're doing.<span><font
color="#888888"><br>
<br>
Mark</font></span>
<div>
<div><br>
<br>
<blockquote type="cite"> <br>
<br>
I'm using berger lipids and that mdp
file for the G_membed<br>
<br>
integrator = md<br>
energygrps = Protein<br>
freezegrps = Protein<br>
freezedim = Y Y Y<br>
energygrp_table<br>
energygrp_excl = Protein Protein<br>
<br>
<br>
<br>
emtol = 1000.0 ; Stop
minimization when the maximum force
< 1000.0 kJ/mol/nm<br>
emstep = 0.01 ; Energy step
size<br>
nsteps = 50000 ;
Maximum number of (minimization) steps
to perform<br>
<br>
; Bond parameters<br>
constraint_algorithm = lincs ;
holonomic constraints <br>
constraints = all-bonds
; all bonds (even heavy atom-H bonds)
constrained<br>
lincs_iter = 1 ;
accuracy of LINCS<br>
lincs_order = 4
; also related to accuracy<br>
; Neighborsearching<br>
ns_type = grid ; search
neighboring grid cels<br>
nstlist = 5 ; 10 fs<br>
rlist = 1.2 ;
short-range neighborlist cutoff (in
nm)<br>
rcoulomb = 1.2 ; short-range
electrostatic cutoff (in nm)<br>
rvdw = 1.2 ; short-range
van der Waals cutoff (in nm)<br>
; Electrostatics<br>
coulombtype = PME ; Particle
Mesh Ewald for long-range
electrostatics<br>
pme_order = 4 ; cubic
interpolation<br>
fourierspacing = 0.16 ; grid
spacing for FFT<br>
pbc = xyz ; 3-D PBC<br>
<br>
<br>
Could you tell me where is the problem
in my case might be?<br>
<br>
<br>
James<br>
<br>
<fieldset></fieldset>
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