Hello Sir,<br><br>The whole point in making an index file was to merge the sol and cl- ions.<br>If i put popc also in the index file then it wont make any much useful group because lipids needs to be defined in a different group as I have read in various archives. Please do correct me if I am wrong.<br>
<br>Thanking you,<br>Pawan<br><br><br><br><div class="gmail_quote">On Thu, Apr 9, 2009 at 10:14 AM, Dallas B. Warren <span dir="ltr"><<a href="mailto:Dallas.Warren@pharm.monash.edu.au">Dallas.Warren@pharm.monash.edu.au</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<div>
<div dir="ltr" align="left"><span><font color="#0000ff" size="2" face="Arial">Well, as the error says, popc isn't defined in the index
file. <span><font color="#0000ff" size="2" face="Arial">Seems grompp is looking for a popc entry in the index file, and can't
find it.</font></span> So, I would hazard to say, you need to define
it.</font></span></div>
<div dir="ltr" align="left"><span><font color="#0000ff" size="2" face="Arial"></font></span> </div>
<div dir="ltr" align="left"><font size="2">Catch ya,<br><br>Dr. Dallas
Warren<br>Department of Pharmaceutical Biology and Pharmacology<br>Pharmacy and
Pharmaceutical Sciences, Monash University<br>381 Royal Parade, Parkville VIC
3010<br><a href="mailto:dallas.warren@pharm.monash.edu.au" target="_blank">dallas.warren@pharm.monash.edu.au</a><br>+61 3 9903
9167<br>---------------------------------<br>When the only tool you own is a
hammer, every problem begins to resemble a nail.</font> </div>
<div><font color="#0000ff" size="2" face="Arial"></font> </div><br>
<blockquote style="border-left: 2px solid rgb(0, 0, 255); padding-left: 5px; margin-left: 5px; margin-right: 0px;">
<div dir="ltr" align="left" lang="en-us">
<hr>
<font size="2" face="Tahoma"><b>From:</b> <a href="mailto:gmx-users-bounces@gromacs.org" target="_blank">gmx-users-bounces@gromacs.org</a>
[mailto:<a href="mailto:gmx-users-bounces@gromacs.org" target="_blank">gmx-users-bounces@gromacs.org</a>] <b>On Behalf Of </b>Pawan
Kumar<br><b>Sent:</b> Thursday, 9 April 2009 2:39 PM<br><b>To:</b>
<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>; Discussion list for GROMACS users<br><b>Subject:</b> Re:
[gmx-users] Membrane protein tutorial<br></font><br></div><div><div></div><div class="h5">
<div></div>Hello sir,<br><br>Thanks for such a explanatory tutorial.<br>I am
stuck with one error now.<br>I have protein, popc, sol and cl- in my
system.<br>I have merged the sol and cl- using make_ndx.<br>But when I run
grompp I get the error like this "popc not defined in the index file".<br>The
grompp command : grompp -f pr.mdp -c box_em.pdb -p topol.top -o
box_pr.tpr<br>Any suggestions please.<br><b><br>pr.mdp file
:</b><br>title
= protein in popc
bilayer<br>cpp
=
/usr/bin/cpp<br>define
= -DPOSRES
-DPOSRES_LIPID<br>constraints
= all-bonds<br>constraint-algorithm=
Lincs<br>integrator
=
md<br>dt
= 0.002
<br>nsteps
= 5000
<br>nstcomm
=
1<br>nstxout
=
50<br>nstvout
=
1000<br>nstfout
=
0<br>nstlog
=
10<br>nstenergy
=
10<br>nstlist
=
10<br>ns_type
=
grid<br>rlist
= 1<br>coulombtype
=
PME<br>rcoulomb
=
1<br>vdw-type
=
Cut-off<br>rvdw
= 1<br>; Berendsen temperature coupling is on in two
groups<br>tcoupl
=
berendsen<br>tc_grps
= Protein POPC
SOL_CL-<br>tau_t
= 0.1 0.1 0.1
<br>ref_t
= 300 300 300<br>; Energy monitoring<br>energygrps
= Protein POPC SOL_CL-<br>; Pressure coupling is
on<br>;Pcoupl
=
berendsen<br>tau_p
= 2.0 2.0<br>compressibility = 4.5e-5
4.5e-5<br>ref_p
= 1.0 1.0<br>Pcoupl_type
= semiisotropic<br>; Generate velocites is on at 300
K.<br>gen_vel
=
yes<br>gen_temp
=
300.0<br>gen_seed
= 173529<br><br>Thanking you,<br>Pawan<br></div></div></blockquote></div>
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