[gmx-users] Fwd: Net charge error

[Justin Lemkul]

On 1/11/15 10:57 AM, Siddhesh Kamat wrote:
> Hello everyone,
> Thanks for the prompt reply. I have attached the .itp and .top files of
> MPNA(monoprotic napthenic acid). This is the error I get on energy
> minimisation:

The mailing list does not accept attachments.  That's why I said provide a link 
for a download.  Post the files somewhere and send the URL.

> command line
> gmx grompp -f minim.mdp -c MPNA_solv.gro -p topol.top -o em.tpr
>
>
> Back Off! I just backed up mdout.mdp to ./#mdout.mdp.14#
>
> NOTE 1 [file minim.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 2203031122
> Generated 331705 of the 331705 non-bonded parameter combinations
> Generating 1-4 interactions: fudge = 0.5
> Generated 331705 of the 331705 1-4 parameter combinations
> Excluding 3 bonded neighbours molecule type 'MPNA'
> Excluding 2 bonded neighbours molecule type 'SOL'
>
> NOTE 2 [file topol.top, line 20]:
>    System has non-zero total charge: 452.808792
>    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.
>
>
>
>
> -------------------------------------------------------
> Program gmx, VERSION 5.0.2
> Source code file:
> /home/canales/gromacs-5.0.2/src/gromacs/gmxpreprocess/grompp.c, line: 603
>
> Fatal error:
> number of coordinates in coordinate file (MPNA_solv.gro, 4883)
>               does not match topology (topol.top, 4884)
>

Be sure your protonation state matches between coordinates and topology.

-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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