[gmx-users] Error in Membrane simulations with POPC bilayer

[J Peterson]

Hi Justin and Anirban,

I started a membrane simulation with POPC bilayer after a training with the
given KALP peptide and DPPC bilayer. I am following both of your tutorials
(mainly the Justin's). I have problem at where I generate a .tpr file for a
DPPC (POPC here)-only system using grompp.

I see another warning on non-matching number of atoms along with the error
that you recommended a safe one.

My error is 

Warning: atom name 3340 in topol_popc.top and popc_128b_H.pdb does not match
(C12 - H2)
Warning: atom name 3341 in topol_popc.top and popc_128b_H.pdb does not match
(C13 - O)
Warning: atom name 3342 in topol_popc.top and popc_128b_H.pdb does not match
(O14 - H1)
Warning: atom name 3343 in topol_popc.top and popc_128b_H.pdb does not match
(C15 - H2)
Warning: atom name 3344 in topol_popc.top and popc_128b_H.pdb does not match
(O16 - O)
Warning: atom name 3345 in topol_popc.top and popc_128b_H.pdb does not match
(C17 - H1)
Warning: atom name 3346 in topol_popc.top and popc_128b_H.pdb does not match
(C18 - H2)
Warning: atom name 3347 in topol_popc.top and popc_128b_H.pdb does not match
(C19 - O)
Warning: atom name 3348 in topol_popc.top and popc_128b_H.pdb does not match
(C20 - H1)
(more than 20 non-matching atom names)

WARNING 1 [file topol_popc.top, line 26]:
  10708 non-matching atom names
  atom names from topol_popc.top will be used
  atom names from popc_128b_H.pdb will be ignored

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 42105.00
Largest charge group radii for Van der Waals: 6.115, 5.932 nm
Largest charge group radii for Coulomb:       6.546, 6.115 nm

WARNING 2 [file em_st.mdp]:
  The sum of the two largest charge group radii (12.661407) is larger than
  rlist (0.900000)

Calculating fourier grid dimensions for X Y Z
Using a fourier grid of 54x56x48, spacing 0.117 0.117 0.119
Estimate for the relative computational load of the PME mesh part: 0.45
This run will generate roughly 34 Mb of data

There were 2 warnings

-------------------------------------------------------
Program grompp, VERSION 4.5.3
Source code file: grompp.c, line: 1563

Fatal error:
Too many warnings (2), grompp terminated.
If you are sure all warnings are harmless, use the -maxwarn option.

Can any one of you help me move from here?

Peterson J

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