[gmx-users] Fatal error in popc simulation: Atomtype LC3 not found

[Justin A. Lemkul]

On 4/25/12 2:07 AM, Shima Arasteh wrote:
> Dear gmx users,
> I want to simulate popc in water. What I have done is:
> 1.Build the popc.top file using the popc.itp parameters and including gmx.ff,
> lipid.itp and spce.itp in it as below;
>
>
> ; Include forcefield parameters
> #include "./gmx.ff/forcefield.itp"
>
> ; Include water topology
> #include "./gmx.ff/spce.itp"
>
> #include "lipid.itp"
>
>
> [ moleculetype ]
> ; Name nrexcl
> POPC 3
>
> [ atoms ]
> ; nr type resnr residu atom cgnr charge mass
> 1 LC3 1 POP C1 0 0.4000 15.0350 ; qtot:0.36
> 2 LC3 1 POP C2 0 0.4000 15.0350 ; qtot:0.72
> .
> .
> .
> [ bonds ]
> ; ai aj funct
> 4 5 1 0.14700E+00 0.37660E+06
> 5 6 1 0.15300E+00 0.33470E+06
> 6 7 1 0.14300E+00 0.25100E+06
> .
> .
> .
>
>
> [ pairs ]
> ; ai aj funct
> 1 6 1
> 2 6 1
> .
> .
> .
>
> [ angles ]
> ; ai aj ak funct
> 4 5 6 1 0.10950E+03 0.46020E+03
> 5 6 7 1 0.10950E+03 0.46020E+03
> 6 7 8 1 0.12000E+03 0.39750E+03
> 7 8 9 1 0.10960E+03 0.39750E+03
>
> 48 49 50 1 0.11100E+03 0.46020E+03
> 1 4 2 1 0.10950E+03 0.33470E+03
> 2 4 3 1 0.10950E+03 0.33470E+03
> 3 4 1 1 0.10950E+03 0.33470E+03
> 1 4 5 1 0.10950E+03 0.37660E+03
> 2 4 5 1 0.10950E+03 0.37660E+03
> 3 4 5 1 0.10950E+03 0.37660E+03
>
> [ dihedrals ]
> ; ai aj ak al funct phi0 cp mult
> 1 4 5 6 1 0.0 3.76 3
> 4 5 6 7 1 0.0 5.85 3
> .
> .
> .
>
> [ dihedrals ]
> ; ai aj ak al funct
> 13 14 32 12 2 35.264 0.33470E+03
> 15 14 17 16 2 0.00000E+00 0.16740E+03
> 34 33 36 35 2 0.00000E+00 0.16740E+03
> 23 24 25 26 2 0.000 167.360
>
>
> [ system ]
> ; name
> POPC in water
>
> [ molecules ]
> ; name number
> POPC 128
> SOL 3802
>
> But I still get the "fatal error : Atomtype LC3 not found ".
> What is the problem? Anybody may help me please?
>

I always had problems when trying to simply #include "lipid.itp" - the 
directives are not in the proper order for the system .top if you do.  The 
better approach is to append the contents of lipid.itp to the appropriate 
directives in ffnonbonded.itp and ffbonded.itp.  See the approach in:

http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/index.html

-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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