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

[Saikat Banerjee]

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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