Please suggest me the exact way to include dppc coordinates in topol.top file.<br><br><div class="gmail_quote">On Wed, Feb 1, 2012 at 5:06 PM, Mark Abraham <span dir="ltr"><<a 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 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>
<fieldset></fieldset>
<br>
</blockquote>
<br>
</div>
</div>
<br>
--<br>
gmx-users mailing list <a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a><br>
<a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>
Please search the archive at <a href="http://www.gromacs.org/Support/Mailing_Lists/Search" target="_blank">http://www.gromacs.org/Support/Mailing_Lists/Search</a>
before posting!<br>
Please don't post (un)subscribe requests to the list. Use the<br>
www interface or send it to <a href="mailto:gmx-users-request@gromacs.org" target="_blank">gmx-users-request@gromacs.org</a>.<br>
Can't post? Read <a href="http://www.gromacs.org/Support/Mailing_Lists" target="_blank">http://www.gromacs.org/Support/Mailing_Lists</a><br>
</blockquote>
</div>
<br>
<br>
<fieldset></fieldset>
<br>
</blockquote>
<br>
</div></div></div>
<br>--<br>
gmx-users mailing list <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>
<a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>
Please search the archive at <a href="http://www.gromacs.org/Support/Mailing_Lists/Search" target="_blank">http://www.gromacs.org/Support/Mailing_Lists/Search</a> before posting!<br>
Please don't post (un)subscribe requests to the list. Use the<br>
www interface or send it to <a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>.<br>
Can't post? Read <a href="http://www.gromacs.org/Support/Mailing_Lists" target="_blank">http://www.gromacs.org/Support/Mailing_Lists</a><br></blockquote></div><br>