[gmx-users] Fatal Error: moleculetype K is redefined

[Venky]

Hi,
While trying to setup a membrane inserted protein simulation I get this
following error while running grompp command.

% grompp -v -f em.mdp -c br1.pdb -p example.top -o br_emin.tpr

Generated 1369 of the 2211 non-bonded parameter combinations
Excluding 3 bonded neighbours for Protein_A 1
Cleaning up temporary file gromppjh3WI9
-------------------------------------------------------
Program grompp, VERSION 3.3.1
Source code file: toppush.c, line: 891

Fatal error:
moleculetype K is redefined
-------------------------------------------------------

But there are no moleculetypes K in my simulation and I have not generated
any ions yet. I also had to do setup other lipids but again ended up in the
same error. Please help...thanks in advance... below are the details of my
input files.

EM.mdp options
--------
title = BR_POPC
cpp = /usr/bin/cpp ; the c pre-processor
define = -DFLEXIBLE
constraints = none
integrator = cg
dt = 0.002 ; ps !
nsteps = 1000
nstlist = 5
ns_type = grid
rlist = 0.9
coulombtype = PME
rcoulomb = 0.9
rvdw = 1.4
fourierspacing = 0.12
fourier_nx = 0
fourier_ny = 0
fourier_nz = 0
pme_order = 4
ewald_rtol = 1e-5
optimize_fft = yes
;
; Energy minimizing stuff
;
emtol = 1000.0
emstep = 0.01

--------------------
TOP File input
----------------


#include "ffgmx.itp"
#include "lipid.itp"
#include "popc.itp"
#include "br.top"     ;; protein topology
#include "ions.itp"

#ifdef FLEX_SPC
#include "flexspc.itp"
#else
#include "spc.itp"
#endif

[ system ]
; name
BR_POPC

[ molecules ]
; name    number
Protein 1
POPC    56
SOL     4412
-----------------------------------


-- 
Venky Krishnamani
Graduate Student,
Dr. Janos K. Lanyi Lab
Univerisity of California, Irvine
Irvine, CA
(949) 232-3021
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