Mark Abraham wrote:
Justin A. Lemkul wrote:
Pawan Kumar wrote:
Hello Sir,
The whole point in making an index file was to merge the sol and cl-
ions.
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.
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:
A new SOL_CL- group is what is needed, not POPC_CL-, probably a typo.
Oops, indeed :)
-Justin
Mark
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/06_equil.html
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.
-Justin
Thanking you,
Pawan
On Thu, Apr 9, 2009 at 10:14 AM, Dallas B. Warren
<dallas.war...@pharm.monash.edu.au
<mailto:dallas.war...@pharm.monash.edu.au>> wrote:
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
can't find it. So, I would hazard to say, you need to define it.
Catch ya,
Dr. Dallas Warren
Department of Pharmaceutical Biology and Pharmacology
Pharmacy and Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3010
dallas.war...@pharm.monash.edu.au
<mailto:dallas.war...@pharm.monash.edu.au>
+61 3 9903 9167
---------------------------------
When the only tool you own is a hammer, every problem begins to
resemble a nail.
------------------------------------------------------------------------
*From:* gmx-users-boun...@gromacs.org
<mailto:gmx-users-boun...@gromacs.org>
[mailto:gmx-users-boun...@gromacs.org
<mailto:gmx-users-boun...@gromacs.org>] *On Behalf Of *Pawan
Kumar
*Sent:* Thursday, 9 April 2009 2:39 PM
*To:* jalem...@vt.edu <mailto:jalem...@vt.edu>; Discussion list
for GROMACS users
*Subject:* Re: [gmx-users] Membrane protein tutorial
Hello sir,
Thanks for such a explanatory tutorial.
I am stuck with one error now.
I have protein, popc, sol and cl- in my system.
I have merged the sol and cl- using make_ndx.
But when I run grompp I get the error like this "popc not
defined in the index file".
The grompp command : grompp -f pr.mdp -c box_em.pdb -p topol.top
-o box_pr.tpr
Any suggestions please.
*
pr.mdp file :*
title = protein in popc bilayer
cpp = /usr/bin/cpp
define = -DPOSRES -DPOSRES_LIPID
constraints = all-bonds
constraint-algorithm= Lincs
integrator = md
dt = 0.002 nsteps =
5000 nstcomm = 1
nstxout = 50
nstvout = 1000
nstfout = 0
nstlog = 10
nstenergy = 10
nstlist = 10
ns_type = grid
rlist = 1
coulombtype = PME
rcoulomb = 1
vdw-type = Cut-off
rvdw = 1
; Berendsen temperature coupling is on in two groups
tcoupl = berendsen
tc_grps = Protein POPC SOL_CL-
tau_t = 0.1 0.1 0.1
ref_t = 300 300 300
; Energy monitoring
energygrps = Protein POPC SOL_CL-
; Pressure coupling is on
;Pcoupl = berendsen
tau_p = 2.0 2.0
compressibility = 4.5e-5 4.5e-5
ref_p = 1.0 1.0
Pcoupl_type = semiisotropic
; Generate velocites is on at 300 K.
gen_vel = yes
gen_temp = 300.0
gen_seed = 173529
Thanking you,
Pawan
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--
========================================
Justin A. Lemkul
Graduate Research Assistant
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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