[gmx-users] Fwd: Gromacs

[saranya]

Respected Sir,
              Though im finshed upto production step of protein metal
complexes, topology file couldnt be created and there is no information
about any atoms in my pdb file.  the created topology file are shown below


;
;    File 'ebolaag.top' was generated
;    By user: onbekend (0)
;    On host: onbekend
;    At date: Wed Oct  7 16:06:22 2015
;
;    This is a standalone topology file
;
;    It was generated using program:
;    pdb2gmx_d - VERSION 4.5
;
;    Command line was:
;    ./pdb2gmx_d -f ebolaag.pdb -o ebolaag.gro -p ebolaag.top -ignh
;
;    Force field was read from the standard Gromacs share directory.
;

; Include forcefield parameters
#include "oplsaa.ff/forcefield.itp"

; Include chain topologies
#include "ebolaag_Protein_chain_A.itp"
#include "ebolaag_Ion_chain_A2.itp"

; Include water topology
#include "oplsaa.ff/tip4p.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 "oplsaa.ff/ions.itp"

[ system ]
; Name
Protein in water

[ molecules ]
; Compound        #mols
Protein_chain_A     1
Ion_chain_A2        1
SOL              4673



I can't understand what is the problem, so pls tell me  what could be the
reason for this.


Sincierly,

*Saranya Vasudevan,*

*Research Scholar,*

*Molecular Quantum Mechanics Laboratory,*

*Department of Physics,*

*Bharathiar University,*

*Coimbatore-46*