[gmx-users] Error in Membrane simulations with POPC bilayer
J Peterson
think_beyond at aol.com
Fri Jul 6 16:48:44 CEST 2012
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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