http://www.gromacs.org/Documentation/Terminology/Blowing_Up#Diagnosing_an_Unstable_System

You have infinite energy in your system, implying a physically impossible starting configuration or a broken topology. Simplify - make sure you can run a system with one peptide, and if you can, revisit however it was that you built the two-peptide system. Simply visualizing the starting coordinates often illustrates what the problem is.

Dear Justin,

Thank you very much for your suggestions. The steepest descent energy minimization step was successfully completed for the single peptide chain.  However, I got the following or the above-mentioned error for two peptide chain of the same sequence.

Enabling TIP4p-like water optimization for 6882 molecules.

Configuring nonbonded kernels...

Configuring standard C nonbonded kernels...

Testing x86_64 SSE2 support... present.

Removing pbc first time

Linking all bonded interactions to atoms

There are 3728 inter charge-group exclusions,

will use an extra communication step for exclusion forces for PME

The initial number of communication pulses is: X 1 Y 1 Z 1

The initial domain decomposition cell size is: X 3.01 nm Y 3.01 nm Z 3.01 nm

The maximum allowed distance for charge groups involved in interactions is:

non-bonded interactions 1.000 nm

two-body bonded interactions (-rdd) 2.356 nm

multi-body bonded interactions (-rdd) 2.356 nm.

Please suggest me. 

Sincerely,

Kalyanashis

Your C-terminal glutamate residues have incomplete carboxylate groups, so the topology is incorrect. You need to generate a correct topology with pdb2gmx and select appropriate terminal types.

Dear Justin,

Thank you very much for your prompt reply. I have carefully checked that there will be 15 atoms in GLU16 and GLU17 residues. LYS18 is C-terminal amino acid residue. I could not understand how the carboxylate groups are incomplete. Please suggest me.

Looking forward to your suggestions. 

In pdb file

ATOM    283 N    GLU A  16      47.107  28.952  45.581  1.00  0.00           N

ATOM    284 H    GLU A  16      46.317  28.362  45.371  1.00  0.00           H

ATOM    285  CA  GLU A  16      48.057  29.082  44.441  1.00  0.00           C

ATOM    286  HA  GLU A  16      49.018  28.668  44.746  1.00  0.00           H

ATOM    287  CB  GLU A  16      47.467  28.182  43.351  1.00  0.00           C

ATOM    288  HB1 GLU A  16      47.555  27.154  43.702  1.00  0.00           H

ATOM    289  HB2 GLU A  16      46.414  28.445  43.254  1.00  0.00           H

ATOM    290  CG  GLU A  16      48.077  28.232  41.941  1.00  0.00           C

ATOM    291  HG1 GLU A  16      48.377  29.254  41.708  1.00  0.00           H

ATOM    292  HG2 GLU A  16      48.947  27.578  41.895  1.00  0.00           H

ATOM    293  CD  GLU A  16      47.027  27.762  40.931  1.00  0.00           C

ATOM    294  OE1 GLU A  16      45.837  28.052  41.141  1.00  0.00           O

ATOM    295  OE2 GLU A  16      47.397  27.142  39.911  1.00  0.00           O

ATOM    296 C    GLU A  16      48.287  30.522  43.931  1.00  0.00           C

ATOM    297 O    GLU A  16      49.437  30.902  43.671  1.00  0.00           O

In aminoacid.rtp file

 [ GLU ]

 [ atoms ]

     N    N           -0.423392    1

     H    H            0.306811    2

    CA    CT           0.031633    3

    HA    H1           0.065100    4

    CB    CT           0.074772    5

   HB1    HC          -0.003535    6

   HB2    HC          -0.003535    7

    CG    CT          -0.033909    8

   HG1    HC          -0.004135    9

   HG2    HC          -0.004135   10

    CD    C            0.765188   11

   OE1    O2          -0.824035   12

   OE2    O2          -0.824035   13

     C    C            0.469735   14

     O    O           -0.592528   15

Sincerely,

Kalyanashis Jana

I see.  The structure did not display correctly for me in VMD.  I'm not sure what the problem is.  Please follow the link I provided before for suggestions.  See if it will minimize in vacuo, etc.

Dear Justin, 

Thank you very much for your suggestion. I am following the procedure written by you.

Sincerely,

Kalyanashis Jana