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

[Esteban Gabriel Vega Hissi]

Hi,
I did the same and the simulations work properly! I think it's a matter of
labels.

Esteban
UNSL
Argentina
--

2010/4/30 Saikat Banerjee <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
>      banskt at yahoo.co.in
> -------------------------------------------------------------------
>
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