[gmx-users] Fwd: Net charge error

[Siddhesh Kamat]

Hello everyone,

links to attchments:
https://drive.google.com/file/d/0B83MUXW1ifjQLVJoalhNR1FRczg/view?usp=sharing
( itp file)
https://drive.google.com/file/d/0B83MUXW1ifjQcWR5Ny1UczZxMUk/view?usp=sharing
(top file)
Regards,
Siddhesh Kamat

On Sun, Jan 11, 2015 at 11:00 AM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> 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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