[gmx-users] Pdb2gmx melts molecules due to bad distances

[GIANMARCO BARTALINI]

Thanks, but it doesn't work. Same problem.

Gianmarco Bartalini

Il 27 nov 2017 14:37, "Justin Lemkul" <jalemkul at vt.edu> ha scritto:

>
>
> On 11/27/17 6:04 AM, GIANMARCO BARTALINI wrote:
>
>> Hello guys, I produced a system "protein + lipid membrane" using the
>> online
>> tool CHARMM-GUI. Since I need to use the Amber force field, I added the
>> Lipids17 force field inside Gromacs. The implementation should work fine,
>> since the conversion of an equilibrated structure produces a nice and
>> correct gro file. But when I try to convert the (not minimized) PDB file
>> that I get from CHARMM-GUI using pdb2gmx, I get a gro structure where many
>> lipid molecules are melted together (due to their bad distances). If I use
>> this structure for a minimization, the calculation stops due to bad
>> energies. Do you know how to solve this issue?
>>
>
> This isn't a pdb2gmx problem so much as it is a quirk of how CHARMM-GUI
> creates lipid membranes. There is almost always overlap between tail atoms
> in the different lipid leaflets. The CHARMM minimizer deals with these just
> fine, but GROMACS almost always chokes. The reason is that GROMACS sets a
> rather aggressive default EM step size of 0.02 nm, whereas the CHARMM
> minimizer defaults to 0.002. Lower the value of emstep and see if it
> proceeds correctly. That has always worked for us.
>
> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Virginia Tech Department of Biochemistry
>
> 303 Engel Hall
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> jalemkul at vt.edu | (540) 231-3129
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>
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