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On 2/02/2012 5:41 PM, Anushree Tripathi wrote:
<blockquote
cite="mid:CAAx43Bw4rJk=jcZJ+zfMNXGtUHyqnLbcC8pFp8BgRBgg-c4NxQ@mail.gmail.com"
type="cite">Please suggest me the exact way to include dppc
coordinates in topol.top file.<br>
</blockquote>
<br>
Start here <a
href="http://www.gromacs.org/Documentation/How-tos/Membrane_Simulations">http://www.gromacs.org/Documentation/How-tos/Membrane_Simulations</a>,
as I think Justin already suggested. You should definitely learn
(about) other people's workflows before attempting to adapt them to
your needs.<br>
<br>
Mark<br>
<br>
<blockquote
cite="mid:CAAx43Bw4rJk=jcZJ+zfMNXGtUHyqnLbcC8pFp8BgRBgg-c4NxQ@mail.gmail.com"
type="cite"><br>
<div class="gmail_quote">On Wed, Feb 1, 2012 at 5:06 PM, Mark
Abraham <span dir="ltr"><<a moz-do-not-send="true"
href="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</a>></span>
wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0
.8ex;border-left:1px #ccc solid;padding-left:1ex">
<div bgcolor="#FFFFFF" text="#000000">
<div class="im"> On 1/02/2012 6:25 PM, Anushree Tripathi
wrote:
<blockquote type="cite">But in coordinate file(.pdb file)
,I am not getting the atoms which belongs to DPPC.</blockquote>
<br>
</div>
You cannot do anything unless you have a coordinate file
that includes DPPC coordinates. I don't know how to express
this any more clearly.
<div class="im"><br>
<br>
<blockquote type="cite">only I have included the name of
dppc.itp file like this:<br>
;Include DPPC chain topology<br>
#include "dppc.itp"<br>
<br>
That's why I have found the atoms wich belongs to DPPC
molecule from dppc.itp file itself.<br>
</blockquote>
<br>
</div>
These numbers are not useful, as I have already explained.<span
class="HOEnZb"><font color="#888888"><br>
<br>
Mark</font></span>
<div>
<div class="h5"><br>
<br>
<blockquote type="cite"> <br>
<br>
<div class="gmail_quote">On Wed, Feb 1, 2012 at 12:40
PM, 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>
wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0
.8ex;border-left:1px #ccc solid;padding-left:1ex">
<div bgcolor="#FFFFFF" text="#000000">
<div> On 1/02/2012 6:04 PM, Anushree Tripathi
wrote:
<blockquote type="cite">When I run the command
(i.e., make_ndx -f em.gro -o index.ndx) ,it
is showing the following options:<br>
0 System : 18379 atoms<br>
1 Protein : 11739 atoms<br>
2 Protein-H : 9135 atoms<br>
3 C-alpha : 1173 atoms<br>
4 Backbone : 3519 atoms<br>
5 MainChain : 4693 atoms<br>
6 MainChain+Cb : 5773 atoms<br>
7 MainChain+H : 5842 atoms<br>
8 SideChain : 5897 atoms<br>
9 SideChain-H : 4442 atoms<br>
10 Prot-Masses : 11739 atoms<br>
11 non-Protein : 6640 atoms<br>
12 Water : 6636 atoms<br>
13 SOL : 6636 atoms<br>
14 non-Water : 11743 atoms<br>
15 Ion : 4 atoms<br>
16 CL : 4 atoms<br>
17 Water_and_ions : 6640 atoms<br>
</blockquote>
<br>
</div>
So your system has 18K atoms, with 11K protein
and the rest solvent and ions. As Justin
suggested, this coordinate file does not have
DPPC in it.
<div><br>
<br>
<br>
<blockquote type="cite">for my work, I used
16|13 then 1|11.lastly I saved it using
'q'.But there is no option for DPPC (as
given in tutorial we have to merge protein
with DPPC).After runing the command (grompp
-f nvt.mdp -c em.gro -p topol.top -n
index.ndx -o nvt.tpr),it is showing error:<br>
<br>
Group DPPC not found in indexfile.<br>
Maybe you have non-default goups in your mdp
file, while not using the '-n' option of
grompp.<br>
In that case use the '-n' option.<br>
<br>
To troubleshoot the error,I have kept one
more group in index.ndx file with number of
atoms which I found from dppc.itp file(at
the end of file) like this<br>
<br>
[DPPC]<br>
1 2 3 4 5 6 7 8 9
10 11 12 13 14 15<br>
16 17 18 19 20 21 22 23 24
25 26 27 28 29 30<br>
31 32 33 34 35 36 37 38 39
40 41 42 43 44 45<br>
46 47 48 49 50<br>
</blockquote>
<br>
</div>
These numbers have to reference the atom numbers
in the coordinate file, not the [moleculetype].
Since you've done the latter, you get the
problem with T-coupling groups. But go back and
use a coordinate file that actually has DPPC in
it.<span><font color="#888888"><br>
<br>
Mark</font></span>
<div><br>
<br>
<blockquote type="cite"><br>
Again after running the grompp command
(grompp -f nvt.mdp -c em.gro -p topol.top -n
index.ndx -o nvt.tpr),I am getting the
following error:<br>
<br>
Atom 1 in multiple T-Coupling groups (1 and
2).<br>
<br>
Please suggest me the reason as well as
solution for this problem.<br>
<br>
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