[gmx-users] Problem in production run

[Justin Lemkul]

On 6/30/15 4:20 AM, Pavithra wrote:
> 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

Likely a visualization artifact.  See 
http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions

> 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.
>

You deleted the ligand?  How did you carry out a simulation of a protein-ligand 
complex?

You have a topology syntax problem.  You shouldn't go hacking things out of it 
to make errors disappear.  You should open up Chapter 5 of the manual and see 
what the required order should be.  If your ligand introduces new atom types, it 
needs to be #included before the protein [moleculetype] (the list archive covers 
all of this, and this case is also explicitly covered in 
http://www.gromacs.org/Documentation/Errors#Invalid_order_for_directive_xxx)

>
>
>
>
>
> *; Include Position restraint file#ifdef POSRES#include "posre.itp"#endif*
>
> *(deleted the ligand topology section from here)*
>

There shouldn't be anything related to a ligand in the protein's restraint file. 
  Be careful of what you're doing, it doesn't seem to make much sense.

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

Included what in the water topology?

>
>
> *;;    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?
>

You've done a lot of things that can lead to total nonsense.  I suggest starting 
over with a better understanding of what's going on, consulting the links above 
and making use of the mailing list archive where similar issues have been discussed.

-Justin

-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==================================================