[gmx-users] Errors during energy minimization of POPC membrane

[Justin Lemkul]

On 10/7/16 12:15 PM, Roshan Shrestha wrote:
> I created a POPC membrane using CHARMM membrane builder, added some water
> into it using gromacs, did not add any ions since it was already neutral,
> then I ran its energy minimization using minim.mdp of lysozyme tutorial.
> However, I ended up with lots of errors like these below after using grompp:
>
>
> *ERROR 9779 [file topol.top, line 161668]:  No default U-B typesERROR 9780
> [file topol.top, line 161669]:  No default U-B typesERROR 9781 [file
> topol.top, line 161671]:  No default U-B typesERROR 9782 [file topol.top,
> line 161672]:  No default U-B typesERROR 9783 [file topol.top, line
> 161674]:  No default U-B typesERROR 9784 [file topol.top, line 161675]:  No
> default U-B typesERROR 9785 [file topol.top, line 161677]:  No default U-B
> typesERROR 9786 [file topol.top, line 161678]:  No default U-B typesERROR
> 9787 [file topol.top, line 161680]:  No default U-B typesERROR 9788 [file
> topol.top, line 161681]:  No default U-B typesExcluding 3 bonded neighbours
> molecule type 'Other'Excluding 2 bonded neighbours molecule type
> 'SOL'Removing all charge groups because cutoff-scheme=VerletThere was 1
> note-------------------------------------------------------Program gmx
> grompp, VERSION 5.1.3Source code file:
> /home/roshan/Downloads/gromacs-5.1.3/src/gromacs/gmxpreprocess/grompp.c,
> line: 1738Fatal error:There were 9788 errors in input file(s)*
>

This suggests something is horrendously broken in your force field.  Any force 
field file from CHARMM-GUI or from our website should have all of the parameters 
necessary to simulate POPC, which is a standard lipid.

-Justin

-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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