[gmx-users] .itp file for DMSO needs to be changed - bug report

[Esteban Gabriel Vega Hissi]

Hi Justin,

You're right. The parameters in ffG53a6 are different from dmso.itp file.
I'll compare the results with the new simulations.
By the way, do you know if ffG53a6 DMSO parameters are updated to those
described in the paper you mention?

Thanks

Esteban

--

2010/4/30 Justin A. Lemkul <jalemkul at vt.edu>

>
>
> Esteban Gabriel Vega Hissi wrote:
>
>> Hi,
>> I did the same and the simulations work properly! I think it's a matter of
>> labels.
>>
>
> Not entirely.  It is a matter of force fields, which sometimes have
> different atom nomenclature.  The dmso.itp file assumes one is using ffgmx.
>  If using Gromos96, the atom types, and perhaps even some of the parameters
> might have to be changed.  There is a paper published about a very good DMSO
> model using Gromos96; I would suggest checking the parameters therein to be
> sure you're actually using a valid model, and not some Frankenforcefield :)
>
> -Justin
>
>
>> Esteban
>> UNSL
>> Argentina
>> --
>>
>> 2010/4/30 Saikat Banerjee <banskt.saikat at gmail.com <mailto:
>> banskt.saikat at gmail.com>>
>>
>>
>>    Hi,
>>
>>    I presume that there is a bug in gromacs-4.0.5.
>>
>>    When tried to run simulations with DMSO molecules there was an error
>>    report, which said:
>>
>>    "Fatal error:
>>    Atomtype SD not found"
>>
>>    I checked extensively for the problem, and found that there is a
>>    small error in the dmso.itp file present in
>>    $GROMACS_INSTALL_DIR/share/gromacs/top/
>>
>>    Line 5 - 10 in dmso.itp file reads,
>>
>>    [ atoms ]
>>    ;   nr    type   resnr  residu  atom    cgnr    charge
>>        1     SD     1      DMSO    SD      1        0.139
>>        2     CD     1      DMSO    CD1     1        0.16
>>        3     OD     1      DMSO    OD      1       -0.459
>>        4     CD     1      DMSO    CD2     1        0.16
>>
>>    I needed to change that to -
>>
>>    [ atoms ]
>>    ;   nr    type   resnr  residu  atom    cgnr    charge  mass
>>        1     SDmso  1      DMSO    SD      1        0.139  32.06000
>>        2     CDmso  1      DMSO    CD1     1        0.16   15.03500
>>        3     ODmso  1      DMSO    OD      1       -0.459  15.99940
>>        4     CDmso  1      DMSO    CD2     1        0.16   15.03500
>>
>>    Please note that the name of the type needed to be changed.
>>
>>    I am not sure if I was doing something wrong, or something was
>>    erroneous in GROMACS. However, the above changes makes it work.
>>
>>    I just thought I would report this issue so that users know where
>>    the problem is. I would like to request the GROMACS team to take
>>    note of it and do the needful.
>>
>>    Thanks,
>>
>>    Saikat B.
>>
>>    --
>> -------------------------------------------------------------------
>>    Saikat Banerjee
>>    Integrated Ph.D student
>>    Prof B. Bagchi's group
>>    Room no. 210
>>    Solid State and Structural Chemistry Unit (SSCU)
>>    Indian Institute of Science
>>    Bangalore-560012
>>          Ph: +91-80-22933305 (lab)
>>         +91-80-23602338 (lab)
>>         +91-9980228606  (mobile)
>>          Alternate e-mail:
>>         saikat at sscu.iisc.ernet.in <mailto:saikat at sscu.iisc.ernet.in>
>>         banskt at yahoo.co.in <mailto:banskt at yahoo.co.in>
>>
>>    -------------------------------------------------------------------
>>
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> --
> ========================================
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
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