[gmx-users] Membrane protein tutorial

[Dallas B. Warren]

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.warren at 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-bounces at gromacs.org
[mailto:gmx-users-bounces at gromacs.org] On Behalf Of Pawan Kumar
	Sent: Thursday, 9 April 2009 2:39 PM
	To: jalemkul at 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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