[gmx-users] Regarding error.

[Javier Cerezo]

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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