[gmx-users] Protein-membrane simulation error.

Justin Lemkul jalemkul at vt.edu
Sat May 21 15:01:55 CEST 2016 


On 5/20/16 6:28 PM, BIJENDRA KHADKA wrote:
> Hello,
> I received the following error while trying to run "Adding ion" step during
> Protein-membrane simulation. Any advice or suggestions will be greatly
> appreciated.
>

You need to tell us all the steps you have taken prior to this point, otherwise 
we're just guessing, which is productive for no one.  In general, you've 
generated a topology that calls for non-existent force field parameters, so 
either you're mixing and matching force fields or you've constructed a force 
field incorrectly.

-Justin

>
> ERROR:
> Command line:
>   gmx grompp -f ions.mdp -c system_box_sol.gro -p topol.top -o ions.tpr
>
>
> NOTE 1 [file ions.mdp, line 17]:
>   ions.mdp did not specify a value for the .mdp option "cutoff-scheme".
>   Probably it was first intended for use with GROMACS before 4.6. In 4.6,
>   the Verlet scheme was introduced, but the group scheme was still the
>   default. The default is now the Verlet scheme, so you will observe
>   different behaviour.
>
>
> Back Off! I just backed up mdout.mdp to ./#mdout.mdp.11#
>
> NOTE 2 [file ions.mdp]:
>   With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
>   that with the Verlet scheme, nstlist has no effect on the accuracy of
>   your simulation.
>
> Setting the LD random seed to 1335440429
> Generated 968 of the 2016 non-bonded parameter combinations
>
> ERROR 1 [file topol.top, line 765]:
>   No default Proper Dih. types
>
>
> ERROR 2 [file topol.top, line 766]:
>   No default Proper Dih. types
>
>
> ERROR 3 [file topol.top, line 768]:
>   No default Proper Dih. types
>
>
> ERROR 4 [file topol.top, line 769]:
>   No default Proper Dih. types
>
>
> ERROR 5 [file topol.top, line 770]:
>   No default Proper Dih. types
>
>
> ERROR 6 [file topol.top, line 771]:
>   No default Proper Dih. types
>
>
> ERROR 7 [file topol.top, line 772]:
>   No default Proper Dih. types
>
>
> ERROR 8 [file topol.top, line 773]:
>   No default Proper Dih. types
>
>
> ERROR 9 [file topol.top, line 774]:
>   No default Proper Dih. types
>
>
> ERROR 10 [file topol.top, line 776]:
>   No default Proper Dih. types
>
>
> ERROR 11 [file topol.top, line 777]:
>   No default Proper Dih. types
>
>
> ERROR 12 [file topol.top, line 778]:
>   No default Proper Dih. types
>
>
> ERROR 13 [file topol.top, line 779]:
>   No default Proper Dih. types
>
>
> ERROR 14 [file topol.top, line 780]:
>   No default Proper Dih. types
>
>
> ERROR 15 [file topol.top, line 781]:
>   No default Proper Dih. types
>
>
> ERROR 16 [file topol.top, line 782]:
>   No default Proper Dih. types
>
>
> ERROR 17 [file topol.top, line 784]:
>   No default Proper Dih. types
>
>
> ERROR 18 [file topol.top, line 785]:
>   No default Proper Dih. types
>
>
> ERROR 19 [file topol.top, line 786]:
>   No default Proper Dih. types
>
>
> ERROR 20 [file topol.top, line 787]:
>   No default Proper Dih. types
>
>
> ERROR 21 [file topol.top, line 789]:
>   No default Proper Dih. types
>
>
> ERROR 22 [file topol.top, line 790]:
>   No default Proper Dih. types
>
>
> ERROR 23 [file topol.top, line 792]:
>   No default Proper Dih. types
>
>
> ERROR 24 [file topol.top, line 793]:
>   No default Proper Dih. types
>
>
> ERROR 25 [file topol.top, line 794]:
>   No default Proper Dih. types
>
>
> ERROR 26 [file topol.top, line 795]:
>   No default Proper Dih. types
>
>
> ERROR 27 [file topol.top, line 797]:
>   No default Proper Dih. types
>
>
> ERROR 28 [file topol.top, line 798]:
>   No default Proper Dih. types
>
>
> ERROR 29 [file topol.top, line 800]:
>   No default Proper Dih. types
>
>
> ERROR 30 [file topol.top, line 801]:
>   No default Proper Dih. types
>
>
> ERROR 31 [file topol.top, line 802]:
>   No default Proper Dih. types
>
>
> ERROR 32 [file topol.top, line 803]:
>   No default Proper Dih. types
>
>
> ERROR 33 [file topol.top, line 805]:
>   No default Proper Dih. types
>
>
> ERROR 34 [file topol.top, line 806]:
>   No default Proper Dih. types
>
>
> ERROR 35 [file topol.top, line 808]:
>   No default Proper Dih. types
>
>
> ERROR 36 [file topol.top, line 809]:
>   No default Proper Dih. types
>
>
> ERROR 37 [file topol.top, line 810]:
>   No default Proper Dih. types
>
>
> ERROR 38 [file topol.top, line 811]:
>   No default Proper Dih. types
>
>
> ERROR 39 [file topol.top, line 813]:
>   No default Proper Dih. types
>
>
> ERROR 40 [file topol.top, line 814]:
>   No default Proper Dih. types
>
>
> ERROR 41 [file topol.top, line 816]:
>   No default Proper Dih. types
>
>
> ERROR 42 [file topol.top, line 817]:
>   No default Proper Dih. types
>
>
> ERROR 43 [file topol.top, line 818]:
>   No default Proper Dih. types
>
>
> ERROR 44 [file topol.top, line 819]:
>   No default Proper Dih. types
>
>
> ERROR 45 [file topol.top, line 821]:
>   No default Proper Dih. types
>
>
> ERROR 46 [file topol.top, line 822]:
>   No default Proper Dih. types
>
>
> ERROR 47 [file topol.top, line 823]:
>   No default Proper Dih. types
>
>
> ERROR 48 [file topol.top, line 824]:
>   No default Proper Dih. types
>
>
> ERROR 49 [file topol.top, line 825]:
>   No default Proper Dih. types
>
>
> ERROR 50 [file topol.top, line 826]:
>   No default Proper Dih. types
>
>
> ERROR 51 [file topol.top, line 827]:
>   No default Proper Dih. types
>
>
> ERROR 52 [file topol.top, line 829]:
>   No default Proper Dih. types
>
>
> ERROR 53 [file topol.top, line 830]:
>   No default Proper Dih. types
>
>
> ERROR 54 [file topol.top, line 831]:
>   No default Proper Dih. types
>
>
> ERROR 55 [file topol.top, line 832]:
>   No default Proper Dih. types
>
>
> ERROR 56 [file topol.top, line 833]:
>   No default Proper Dih. types
>
>
> ERROR 57 [file topol.top, line 834]:
>   No default Proper Dih. types
>
>
> ERROR 58 [file topol.top, line 835]:
>   No default Proper Dih. types
>
>
> ERROR 59 [file topol.top, line 837]:
>   No default Proper Dih. types
>
>
> ERROR 60 [file topol.top, line 838]:
>   No default Proper Dih. types
>
> Excluding 3 bonded neighbours molecule type 'Protein'
> Excluding 3 bonded neighbours molecule type 'DPPC'
> Excluding 2 bonded neighbours molecule type 'SOL'
>
> NOTE 3 [file topol.top, line 930]:
>   System has non-zero total charge: 4.000000
>   Total charge should normally be an integer. See
>   http://www.gromacs.org/Documentation/Floating_Point_Arithmetic
>   for discussion on how close it should be to an integer.
>
>
>
> Removing all charge groups because cutoff-scheme=Verlet
>
> There were 3 notes
>
> -------------------------------------------------------
> Program gmx grompp, VERSION 5.1.2
> Source code file:
> /home/guptalab/gromacs-5.1.2/src/gromacs/gmxpreprocess/grompp.c, line: 1738
>
> Fatal error:
> There were 60 errors in input file(s)
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
> -------------------------------------------------------
>
>
> --
>

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

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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