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

[Justin A. Lemkul]

On 7/6/12 10:48 AM, J Peterson wrote:
> 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?
>

The order of your [molecules] directive does not agree with the contents of the 
coordinate file.  What you're seeing is a mismatch between lipid atom names and 
water (O, H1, and H2).  The second warning may or may not be problematic.  If 
your charge groups are split across periodic boundaries, they will be 
reconstructed properly.  If your molecules are already whole, then you have a 
separate issue.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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