[gmx-users] Regarding error.

Seera Suryanarayana palusoori at gmail.com
Wed Jun 6 10:51:02 CEST 2012

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

                                 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"

; Position restraint for each water oxygen
[ position_restraints ]
;  i funct       fcx        fcy        fcz
   1    1       1000       1000       1000

; 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,
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