It seems that redefinition comes from including tow different ions.itp
files, here:
; Include topology for ions
#include "gromos43a1.ff/ions.itp"
#include "ions.itp"
Javier
El 06/06/12 10:51, Seera Suryanarayana escribió:
Dear all gromacs users,
After added the counter ions to the
top file and further i used 'grompp' commond,i got the following error.
Fatal error:
moleculetype CU1 is
redefined.
This error occurs due the duplication
of CU1 in .top file. But i cannot find that error in my .top file.Here
i am sending my .top file. Kindly tell me how to overcome this error.
;
; File '1UZ9.top' was generated
; By user: onbekend (0)
; On host: onbekend
; At date: Thu Jun 7 13:55:15 2012
;
; This is a standalone topology file
;
; It was generated using program:
; pdb2gmx - VERSION 4.5.5
;
; Command line was:
; pdb2gmx -f 1UZ9.pdb -o 1UZ9.gro -p 1UZ9.top
;
; Force field was read from the standard Gromacs share directory.
;
; Include forcefield parameters
#include "gromos43a1.ff/forcefield.itp"
; Include chain topologies
#include "1UZ9_Protein_chain_A.itp"
#include "1UZ9_Protein_chain_B.itp"
; Include water topology
#include "gromos43a1.ff/spc.itp"
#ifdef POSRES_WATER
; Position restraint for each water oxygen
[ position_restraints ]
; i funct fcx fcy fcz
1 1 1000 1000 1000
#endif
; Include topology for ions
#include "gromos43a1.ff/ions.itp"
#include "ions.itp"
[ system ]
; Name
Protein in water
[ molecules ]
; Compound #mols
Protein_chain_A 1
Protein_chain_B 1
SOL 13532
NA charge 3
/Add NA ions
Thanks and regards
Suryanarayana Seera,
JRF,
India.
--
Javier CEREZO BASTIDA
PhD Student
Physical Chemistry
Universidad de Murcia
Murcia (Spain)
Tel: (+34)868887434
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