[gmx-users] Atomtype C not found

[Justin Lemkul]

On 5/7/13 1:04 PM, Sun Moon wrote:
> Hi
>
> I have been using the lipids from Prof Tieleman's website and (using Berger Lipids) in gromacs 4.5.4  I want to try the grompp tool but have encountered this problem:
>
> Fatal error:
> Atomtype C not found
>
>

This atomtype belongs to protein functional groups.  In lipid.itp, nonbonded 
parameters are defined for protein-lipid interactions.  If you do not need any 
protein-specific terms, delete that section of lipid.itp.

-Justin

> 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
>
> lipid.itpis as the following:
>
> [ defaults ]
> 1       1
> [ atomtypes ]
> ;name     mass     charge ptype  c6           c12
>     LO    15.9994    0.000  A 2.36400e-03 1.59000e-06 ;carbonyl O, OPLS
>    LOM    15.9994    0.000  A 2.36400e-03 1.59000e-06 ;carboxyl O, OPLS
>    LNL    14.0067    0.000  A 3.35300e-03 3.95100e-06 ;Nitrogen, OPLS
>     LC    12.0110    0.000  A 4.88800e-03 1.35900e-05 ;Carbonyl C, OPLS
>    LH1    13.0190    0.000  A 4.03100e-03 1.21400e-05 ;CH1, OPLS
>    LH2    14.0270    0.000  A 7.00200e-03 2.48300e-05 ;CH2, OPLS
> …
> DOPC.itpisas the following:
>   [ moleculetype ]
> ; Name   nrexcl
> DOPC     3
> [ atoms ]
> ;   nr    type   resnr  residu    atom    cgnr        charge          mass
>       1     LC3       1    DOPC      C1       0         0.4000   15.0350         ; qtot:0.36
>       2     LC3       1    DOPC      C2       0         0.4000   15.0350         ; qtot:0.72
>       3     LC3       1    DOPC      C3       0         0.4000   15.0350         ; qtot:1.08
>       4     LNL       1    DOPC      N4       0        -0.5000   14.0067 ; qtot:0.76
>       5     LH2       1    DOPC      C5       0         0.3000   14.0270         ; qtot:1.0
>       6     LC2       1    DOPC      C6       1         0.4000   14.0270         ; qtot:1.0
> ..
> DOPC.grofile as the following:
>
> 128 DOPC in water
> 21387
>      1DOPC    C1    1   4.048   0.461   2.197 -0.4628 -0.6241 -0.6552
>      1DOPC    C2    2   4.064   0.596   2.395 -0.1879  0.0104 -0.0154
>      1DOPC    C3    3   4.110   0.366   2.405 -0.5498 -0.8024 -0.0627
>      1DOPC    N4    4   4.022   0.466   2.341  0.5789 -0.0490 -0.4766
>      1DOPC    C5    5   3.877   0.457   2.361  0.5625  0.0560 -0.5460
>      1DOPC    C6    6   3.823   0.315   2.343  0.0671  0.1818 -0.0962
> …..
> Many thanks for your help in advance!
> Sun
>

-- 
========================================

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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