[gmx-users] Problem in production run

[Pavithra]

Dear Gromacs users and experts,

Newbie here.
This is my first simulation.
I followed Bevan's lab protein-ligand simulation tutorial.
I analysed after em, nvt and npt s per the tutorial and found everything
was okay.
After ns of production run, he complex is not together. I used ACPYPE to
create ligand topology and used amber99sbff for my protein.
I don't have a clue where the probem might me.
could it be the errror in mdp file or with my protein?


I have included my Topol.top, all *.mdp files *itps file here (
http://dropcanvas.com/#tG966EaQ58DlWD)

please let me know if I have to send any other files.

*FYI: *
During first em, the grompp showed me the below error.

*------------------------------*










*-------------------------Program grompp, VERSION 4.5.7Source code file:
topio.c, line: 656Fatal error:Syntax error - File DAP_GMX.itp, line 3Last
line read:'[ atomtypes ]'Invalid order for directive atomtypesFor more
information and tips for troubleshooting, please check the GROMACSwebsite
at http://www.gromacs.org/Documentation/Errors
<http://www.gromacs.org/Documentation/Errors>------------------------------*
*-------------------------*

I opened topol.top file and deleted the ligand topology section at the end.






*; Include Position restraint file#ifdef POSRES#include "posre.itp"#endif*

*(deleted the ligand topology section from here)*




*; Include water topology#include "amber99sb.ff/tip3p.itp"*
included it here
























*;;    File 'topol.top' was generated;    By user: onbekend (0);    On
host: onbekend;    At date: Fri Jun 26 16:30:35 2015;;    This is a
standalone topology file;;    It was generated using program:;    pdb2gmx -
VERSION 4.5.7;;    Command line was:;    pdb2gmx -f 3GEN_final.pdb -o
3GEN_processed.gro -water tip3p ;;    Force field was read from the
standard Gromacs share directory.;; Include forcefield parameters#include
"amber99sb.ff/forcefield.itp"#include "DAP.itp"[ moleculetype ];
Name            nrexclProtein             3*


Doing this fixed the grompp error.
But, Could this be the reason for my result?

please help...

-- 
regards,
Pavithra.