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:
[email protected]
[email protected]
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