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

Saikat Banerjee banskt.saikat at gmail.com
Fri Apr 30 10:44:59 CEST 2010


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.


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

 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
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20100430/5baef1c1/attachment.html>

More information about the gromacs.org_gmx-users mailing list