Respected Sir,<br><br>Greetings from Pawan.<br>It has worked now.<br>I dint edit the index file before also. The problem was with the .mdp file. It was recognising lipids as POP and I gave as POPC in the .mdp file. Now there are no more errors.<br>
Thanks a lot.<br><br>Thanking you,<br>Pawan<br><br><div class="gmail_quote">On Thu, Apr 9, 2009 at 3:35 PM, Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</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 class="im"><br>
<br>
Pawan Kumar wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
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>
</blockquote>
<br></div>
What you need is a POPC_CL- group in addition to the other standard groups. There is a page in my tutorial (which you referenced earlier) that describes exactly how to do this:<br>
<br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/06_equil.html" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/06_equil.html</a><br>
<br>
So your index file should contain System, all the relevant protein groups, POPC, SOL, CL-, and SOL_CL-. If you are considering manually modifying this file in some way (as I am guessing you have), don't.<br>
<br>
-Justin<br>
<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Thanking you,<br>
Pawan<div class="im"><br>
<br>
<br>
<br>
On Thu, Apr 9, 2009 at 10:14 AM, Dallas B. Warren <<a href="mailto:Dallas.Warren@pharm.monash.edu.au" target="_blank">Dallas.Warren@pharm.monash.edu.au</a> <mailto:<a href="mailto:Dallas.Warren@pharm.monash.edu.au" target="_blank">Dallas.Warren@pharm.monash.edu.au</a>>> wrote:<br>
<br>
Well, as the error says, popc isn't defined in the index file. Seems grompp is looking for a popc entry in the index file, and<br>
can't find it. So, I would hazard to say, you need to define it.<br>
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></div>
<mailto:<a href="mailto:dallas.warren@pharm.monash.edu.au" target="_blank">dallas.warren@pharm.monash.edu.au</a>><div class="im"><br>
+61 3 9903 9167<br>
---------------------------------<br>
When the only tool you own is a hammer, every problem begins to<br>
resemble a nail.<br>
<br>
------------------------------------------------------------------------<br>
*From:* <a href="mailto:gmx-users-bounces@gromacs.org" target="_blank">gmx-users-bounces@gromacs.org</a><br>
<mailto:<a href="mailto:gmx-users-bounces@gromacs.org" target="_blank">gmx-users-bounces@gromacs.org</a>><br>
[mailto:<a href="mailto:gmx-users-bounces@gromacs.org" target="_blank">gmx-users-bounces@gromacs.org</a><br>
<mailto:<a href="mailto:gmx-users-bounces@gromacs.org" target="_blank">gmx-users-bounces@gromacs.org</a>>] *On Behalf Of *Pawan Kumar<br>
*Sent:* Thursday, 9 April 2009 2:39 PM<br></div>
*To:* <a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a> <mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>>; Discussion list<div><div></div><div class="h5"><br>
for GROMACS users<br>
*Subject:* Re: [gmx-users] Membrane protein tutorial<br>
<br>
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<br>
defined in the index file".<br>
The grompp command : grompp -f pr.mdp -c box_em.pdb -p topol.top<br>
-o box_pr.tpr<br>
Any suggestions please.<br>
*<br>
pr.mdp file :*<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 nsteps = 5000 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>
<br>
<br>
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-- <br><div class="im">
========================================<br>
<br>
Justin A. Lemkul<br>
Graduate Research Assistant<br>
ICTAS Doctoral Scholar<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> | (540) 231-9080<br>
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