I am new user of Gromacs. I am using Gromacs 5.0.7 version for my MD simulations.

I want to visualize the conformational changes of my protein in the vicinity of membrane. I used popc membrane from Tieleman's website.

I downloaded the following files from his website.

1. popc128a.pdb

2. lipid.itp

3. example2.top (modified accordingly to include the popc.itp instead of dppc.itp for pure popc molecules and spc waters; 128 popc and 2460 spc water molecules)

I am using GROMOS96 53a6 forcefield for the simulations. Created a new directory within the working directory named GROMOS96 53a6_lipid.ff and copied all the files from the GROMOS96 53a6.ff folder. I edited the ffbonded.itp and ffnonbonded.itp files accordingly as mentioned in the tutorials for KALP in DPPC (I included the popc.itp in the .top file). When I run grompp it gives the following error:

gmx grompp -f minim.mdp -c popc128a.gro -p topol_popc.top -o em.tpr -maxwarn 1

GROMACS: gmx grompp, VERSION 5.0.7

GROMACS is written by:

Emile Apol Rossen Apostolov Herman J.C. Berendsen Par Bjelkmar

Aldert van Buuren Rudi van Drunen Anton Feenstra Sebastian Fritsch

Gerrit Groenhof Christoph Junghans Peter Kasson Carsten Kutzner

Per Larsson Justin A. Lemkul Magnus Lundborg Pieter Meulenhoff

Erik Marklund Teemu Murtola Szilard Pall Sander Pronk

Roland Schulz Alexey Shvetsov Michael Shirts Alfons Sijbers

Peter Tieleman Christian Wennberg Maarten Wolf

and the project leaders:

Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel

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Uppsala University, Stockholm University and

the Royal Institute of Technology, Sweden.

check out http://www.gromacs.org for more information.

GROMACS is free software; you can redistribute it and/or modify it

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GROMACS: gmx grompp, VERSION 5.0.7

Executable: /usr/local/gromacs/bin/gmx

Library dir: /usr/local/gromacs/share/gromacs/top

Command line:

gmx grompp -f minim.mdp -c popc128a.gro -p topol_popc.top -o em.tpr -maxwarn 1

Ignoring obsolete mdp entry 'title'

Back Off! I just backed up mdout.mdp to ./#mdout.mdp.5#

Setting the LD random seed to 1495542649

WARNING 1 [file lipid.itp, line 12]:

Overriding atomtype LO

WARNING 2 [file lipid.itp, line 13]:

Overriding atomtype LOM

WARNING 3 [file lipid.itp, line 14]:

Overriding atomtype LNL

WARNING 4 [file lipid.itp, line 15]:

Overriding atomtype LC

WARNING 5 [file lipid.itp, line 16]:

Overriding atomtype LH1

WARNING 6 [file lipid.itp, line 17]:

Overriding atomtype LH2

WARNING 7 [file lipid.itp, line 18]:

Overriding atomtype LP

WARNING 8 [file lipid.itp, line 19]:

Overriding atomtype LOS

WARNING 9 [file lipid.itp, line 20]:

Overriding atomtype LP2

WARNING 10 [file lipid.itp, line 21]:

Overriding atomtype LP3

WARNING 11 [file lipid.itp, line 22]:

Overriding atomtype LC3

WARNING 12 [file lipid.itp, line 23]:

Overriding atomtype LC2

Generated 825 of the 2346 non-bonded parameter combinations

Excluding 3 bonded neighbours molecule type 'POPC'

Excluding 2 bonded neighbours molecule type 'SOL'

Removing all charge groups because cutoff-scheme=Verlet

Analysing residue names:

There are: 128 Other residues

There are: 2460 Water residues

Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups...

Number of degrees of freedom in T-Coupling group rest is 34725.00

Calculating fourier grid dimensions for X Y Z

Using a fourier grid of 52x52x60, spacing 0.120 0.119 0.115

Estimate for the relative computational load of the PME mesh part: 0.21

This run will generate roughly 1 Mb of data

There were 12 warnings

-------------------------------------------------------

Program gmx, VERSION 5.0.7

Source code file: /home/gromacs/Downloads/gromacs-5.0.7/src/gromacs/gmxpreprocess/grompp.c, line: 2092

Fatal error:

Too many warnings (12), gmx terminated.

If you are sure all warnings are harmless, use the -maxwarn option.

For more information and tips for troubleshooting, please check the GROMACS

website at http://www.gromacs.org/Documentation/Errors

I also want to orient my protein such a way that it should not be placed inside the membrane and it should be lie in between the spc water molecules. How can I do this and please provide me the appropriate command to orient my protein is that manner, because the -princ command will orient the protein in the z axis which is normal to the plane of the membrane.

Anyone can help me in overcoming this fatal error will be appreciated.