[gmx-users] Make an index file

[Shima Arasteh]

Actually, I am confused somehow. 

I want to equilibrate the system. It contains popc and water. To equilibrate it, using .mdp file I use the nvt.mdp file as below.

title        = NVT equilibration for POPC
define        = -DPOSRES    ; position restrain the protein
; Run parameters
integrator    = md        ; leap-frog integrator
nsteps        = 50000        ; 2 * 50000 = 100 ps
dt            = 0.002        ; 2 fs
; Output control
nstxout        = 100        ; save coordinates every 0.2 ps
nstvout        = 100        ; save velocities every 0.2 ps
nstenergy    = 100        ; save energies every 0.2 ps
nstlog        = 100        ; update log file every 0.2 ps
; Bond parameters
continuation    = no            ; first dynamics run
constraint_algorithm = lincs    ; holonomic constraints 
constraints    = all-bonds            ; all bonds (even heavy atom-H bonds) constrained
lincs_iter    = 1                    ; accuracy of LINCS
lincs_order    = 4                    ; also related to accuracy
; Neighborsearching
ns_type        = grid        ; search neighboring grid cels
nstlist        = 5            ; 10 fs
rlist        = 1.2        ; short-range neighborlist cutoff (in nm)
rcoulomb    = 1.2        ; short-range electrostatic cutoff (in nm)
rvdw        = 1.2        ; short-range van der Waals cutoff (in nm)
; Electrostatics
coulombtype    = PME        ; Particle Mesh Ewald for long-range electrostatics
pme_order    = 4            ; cubic interpolation
fourierspacing    = 0.16        ; grid spacing for FFT
; Temperature coupling is on
tcoupl        = V-rescale                ; modified Berendsen thermostat
tc-grps        = POPC SOL    ; two coupling groups - more accurate
tau_t        = 0.1    0.1                ; time constant, in ps
ref_t        = 323     323                ; reference temperature, one for each group, in K
; Pressure coupling is off
pcoupl        = no         ; no pressure coupling in NVT
; Periodic boundary conditions
pbc            = xyz        ; 3-D PBC
; Dispersion correction
DispCorr    = EnerPres    ; account for cut-off vdW scheme
; Velocity generation
gen_vel        = yes        ; assign velocities from Maxwell distribution
gen_temp    = 323        ; temperature for Maxwell distribution
gen_seed    = -1        ; generate a random seed




I enter this command:
# grompp -f nvt.mdp -c em.gro -p popc.top -o nvt.tpr

Getting this fatal error:
Group POPC not found in index file.
Group names must match either [moleculetype] names
or custom index group names,in which case you
must supply an index file to the '-n' option of grompp. 


I don't need index file, do I?  What is the problem with my .mdp file?

Cheers,
Shima






________________________________
 From: Justin A. Lemkul <jalemkul at vt.edu>
To: Discussion list for GROMACS users <gmx-users at gromacs.org> 
Sent: Sunday, April 29, 2012 3:10 AM
Subject: Re: [gmx-users] Make an index file
 


On 4/28/12 2:06 PM, Peter C. Lai wrote:
> #2
>
> Generally a good idea to keep the names consistent, however - why are you using
> POP in the coordinate file instead of POPC?

If it is a .pdb file, the standard residue name occupies 3 characters.  Many 
files (including those from Tieleman) are distributed with such names.

To the OP's original question - the commands you issue depend on what you're 
trying to achieve.  What group do you need to create?

-Justin

> --
> Sent from my Android phone with K-9 Mail. Please excuse my brevity.
>
> Shima Arasteh <shima_arasteh2001 at yahoo.com> wrote:
>
>     Dear gmx users,
>     I want to simulate POPC in water. In equilibration step, I have to make an
>     index file. But when I enter this command, I do not know to choose which
>     group to make a suitable .ndx file which matches the molecule types and
>     molecules sections in .top file .
>
>     The .top file contains these:
>
>
>     [ moleculetype ]
>     ; Name nrexcl
>     POPC 3
>     .
>     .
>     .
>     .
>     [ system ]
>     ; name
>     POPC in water
>
>     [ molecules ]
>     ; name number
>     POPC 128
>     SOL 3800
>
>
>     It is the command I enter:
>     # make_ndx -f em.gro -o index.ndx
>     0 System : 18056 atoms
>     1 Other : 6656 atoms
>     2 POP : 6656 atoms
>     3 Water : 11400 atoms
>     4 SOL : 11400 atoms
>     5 non-Water : 6656 atoms
>
>     nr : group ! 'name' nr name 'splitch' nr Enter: list groups
>     'a': atom & 'del' nr 'splitres' nr 'l': list residues
>     't': atom type | 'keep' nr 'splitat' nr 'h': help
>     'r': residue 'res' nr 'chain' char
>     "name": group 'case': case sensitive 'q': save and quit
>     'ri': residue index
>
>     Now, what is the correct answer? Anybody can suggest me?
>
>     Thanks in advance,
>     Shima
>     ge
>
>
>

-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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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