[gmx-users] Fwd: Net charge error

[Justin Lemkul]

On 1/11/15 11:08 AM, Siddhesh Kamat wrote:
> Hello everyone,
>
> links to attchments:
> https://drive.google.com/file/d/0B83MUXW1ifjQLVJoalhNR1FRczg/view?usp=sharing
> ( itp file)

Your topology format is wrong.  You don't have a residue name column:

; nr     type       resnr  atom   cgnr  charge     mass      typeB    chargeB 
    massB
   1    opls_135    1        C       1   -0.18     12.011

The residue name comes between residue number and atom name.

I'm surprised grompp even reads the topology, but the net effect is as I 
suspected - the mass column is interpreted as charge, hence the error you see.

-Justin

> 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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-- 
==================================================

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

==================================================