[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
[phone]
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[Dallas B. Warren]

-------------------------------------------------------
Program grompp, VERSION 3.3.1
Source code file: toppush.c, line: 891

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

I believe this error is due to your forcefield files, the .itp files
that you have included. You have some how doubled up. May be trace
back through each .itp file that you have included.

Was just trying to do a search of the list to check to ensure that was
correct, but with the new website doesn't appear to be working correctly
yet.

Hope that helps some.

Catch ya,

Dr. Dallas Warren
Lecturer
Department of Pharmaceutical Biology and Pharmacology
Victorian College of Pharmacy, Monash University
381 Royal Parade, Parkville VIC 3010
dallas.warren at vcp.monash.edu.au
[phone]
---------------------------------
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