[gmx-users] .itp file for DMSO needs to be changed - bug report
Justin A. Lemkul
jalemkul at vt.edu
Fri Apr 30 13:57:46 CEST 2010
Esteban Gabriel Vega Hissi wrote:
> 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?
>
Not in any pre-built .itp file that I know of, but the .rtp entry for DMSO in
ffG53a6.rtp appears to have the correct charges. I assume, if you check the
atom types, that these are correct, as well.
-Justin
> Thanks
>
> Esteban
>
> --
>
> 2010/4/30 Justin A. Lemkul <jalemkul at vt.edu <mailto: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> <mailto: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>
> <mailto:saikat at sscu.iisc.ernet.in
> <mailto:saikat at sscu.iisc.ernet.in>>
> banskt at yahoo.co.in <mailto:banskt at yahoo.co.in>
> <mailto: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 <http://vt.edu> | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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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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