[gmx-users] Atomtype OW not found

[Justin Lemkul]

On 5/11/13 5:37 AM, Sun Moon wrote:
> Hi,
> I am doing pure membrane simulation in DOPC environment (using Berger
> Lipids) in Gromacs 4.0.7  I want to try the grompp tool but have
> encountered this problem:
>
> Fatal error:
> Atomtype OW  not found
>
> Topology file is as
> the following:
> #include "lipid.itp"
> #include "dopc.itp"
> #include "spc.itp"
> #include "ions.itp"
> '[ system ]'
> ; name
> DOPC bilayer in water
> '[ molecules ]'
> ; name  number
> DOPC      128
> SOL       4825
> ……………….
> Inlipid.itp file, lipid-SPC/SPCE interactions is defined:
> ;;
> lipid-SPC/SPCE interactions
>     LO    OW    1 2.50200e-03  2.06700e-06
>    LOM    OW    1 2.50200e-03  2.06700e-06
>    LNL    OW    1 2.98000e-03  3.25900e-06
>     LC    OW    1 3.59800e-03  6.04400e-06
>    LH1    OW    1 3.26800e-03  5.71200e-06
>    LH2    OW    1 4.30700e-03  8.17000e-06
>     LP    OW    1 4.92600e-03  8.21000e-06
>    LOS    OW    1 2.60500e-03  2.24100e-06
> …….
> Spc.itpfile from gromos
> FF as the following:
> [ moleculetype ]
> ; molname        nrexcl
> SOL                2
> [ atoms ]
> ;   nr   type  resnr residue  atom   cgnr     charge       mass
>       1     OW      1    SOL     OW      1      -0.82
>       2     HW      1    SOL    HW1      1       0.41
>       3     HW      1    SOL    HW2      1       0.41
> …
> …………………….
> dopc.groas the following:
> ….
> 129SOL     OW 6913   4.231   0.169   1.664 -0.1323 -0.0792  0.5040
>   129SOL    HW1 6914   4.146   0.202   1.704 -0.3042  0.1272 -0.0232
>   129SOL    HW2 6915   4.263   0.089   1.715 -0.7744 -0.3135  0.5523
>   130SOL     OW 6916   4.513   4.020   6.355  0.3593 -0.2561  0.3581
>    130SOL    HW1 6917   4.591   3.980   6.403 -0.2604 -0.1715  1.4756
>    130SOL    HW2 6918   4.545   4.090   6.291  1.1718  0.0930  1.1277
> ……..
> What should I do?
>

You need to introduce OW (and probably HW) as valid atom types within the force 
field.  The lipid.itp file was created to be used in conjunction with a Gromos 
parameter set (originally Gromos87, but can also be used with Gromos96) that 
takes care of protein and water atom types.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Research Scientist
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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