[gmx-users] Atomtype OW not found - spc water model
Carlos Navarrro Retamal
cnavarro at utalca.cl
Tue Apr 8 17:24:08 CEST 2014
Hello everyone,
I'm trying to perform a MD of a mixture of solvent (in my case glycerol+water).
In order to do that i first obtained the parameters of glycerol on CHARMM on here -> par_all36_carb.prm. To use this parameters on gromacs i used the psf2topol.py script ->https://github.com/resal81/PyTopol, generating a .top and a .itp file respectively.
Just to try these files, i create a box with 2 molecules of glycerol and add 106 water molecules (SPC)-> Gly_solv.gro file.
Finally, when i edit the topol.top file i add the next line: #include "charmm27.ff/spc.itp", to include the parameters of the SPC water model, but when i run grommp to make a minimization of the system i got the next error message:
> Fatal error:
> Atomtype OW not found
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
but if i remove the water (and of course the include line into the topol.top file) grommp works just fine :/
I really don't know what may be happening.
Hope someone can help me.
Cheers,
ps-
These are my files:
topol.top
> ; Gly_solv.gro
>
> ;Include forcefield parameters
> #include "glycerol.itp"
> #include "itp_mol_01.itp"
> #include "charmm27.ff/spc.itp"
>
> [ system ]
> GlycerolSPC in water
>
> [ molecules ]
> GLY 2
> SOL 106
glycerol.itp
> [ defaults ] ;
> ;nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ
> 1 2 yes 1.0 1.0
> [ atomtypes ]
> CC322 6 12.0110 0.1 A 0.358141284692 0.2343040
> HCA2 1 1.0080 0.1 A 0.238760856462 0.1464400
> OC311 8 15.9994 -0.7 A 0.314487247504 0.8037464
> HCP1 1 1.0080 0.4 A 0.040001352445 0.1924640
> CC312 6 12.0110 0.1 A 0.356359487256 0.1338880
> HCA1 1 1.0080 0.1 A 0.238760856462 0.1882800
>
> [ nonbond_params ]
>
> [ pairtypes ]
> CC322 CC322 1 0.338541512893 0.041840000000
> CC322 HCA2 1 0.288651184677 0.078275472531
> CC322 OC311 1 0.326514380198 0.183381431383
> CC322 HCP1 1 0.189271432669 0.089736802707
> CC322 CC312 1 0.338541512893 0.041840000000
> CC322 HCA1 1 0.288651184677 0.088756043175
> HCA2 CC312 1 0.288651184677 0.078275472531
> OC311 CC312 1 0.326514380198 0.183381431383
> HCP1 CC312 1 0.189271432669 0.089736802707
> CC312 CC312 1 0.338541512893 0.041840000000
> CC312 HCA1 1 0.288651184677 0.088756043175
>
> [ bondtypes ]
> CC322 OC311 1 0.1420 334720.0
> CC322 HCA2 1 0.1111 258571.2
> CC322 CC312 1 0.1485 186188.0
> OC311 HCP1 1 0.0960 456056.0
> CC312 HCA1 1 0.1111 258571.2
> CC312 OC311 1 0.1420 334720.0
>
> [ angletypes ]
> CC322 CC312 CC322 5 111.0000 376.56000 0.00000 0.00000
> CC322 CC312 OC311 5 108.0000 633.45760 0.00000 0.00000
> CC322 CC312 HCA1 5 110.1000 288.69600 0.21790 18853.10400
> CC322 OC311 HCP1 5 106.0000 418.40000 0.00000 0.00000
> HCA2 CC322 CC312 5 110.1000 279.74224 0.21790 18853.10400
> HCA2 CC322 HCA2 5 109.0000 297.06400 0.18020 4518.72000
> OC311 CC322 CC312 5 106.0000 418.40000 0.00000 0.00000
> OC311 CC322 HCA2 5 108.8900 460.24000 0.00000 0.00000
> CC312 OC311 HCP1 5 106.0000 418.40000 0.00000 0.00000
> HCA1 CC312 OC311 5 108.8900 460.24000 0.00000 0.00000
>
> [ dihedraltypes ]
> CC322 CC312 OC311 HCP1 9 0.00 1.46440 1
> CC322 CC312 OC311 HCP1 9 0.00 1.54808 2
> CC322 CC312 OC311 HCP1 9 180.00 0.79496 3
> CC322 CC312 CC322 HCA2 9 0.00 0.83680 3
> CC322 CC312 CC322 OC311 9 0.00 1.46440 1
> CC322 CC312 CC322 OC311 9 0.00 2.88696 2
> CC322 CC312 CC322 OC311 9 180.00 11.67336 3
> HCA2 CC322 OC311 HCP1 9 0.00 0.75312 3
> HCA2 CC322 CC312 HCA1 9 0.00 0.83680 3
> HCA2 CC322 CC312 OC311 9 0.00 0.58576 3
> OC311 CC322 CC312 HCA1 9 0.00 0.58576 3
> OC311 CC322 CC312 OC311 9 180.00 5.60656 1
> OC311 CC322 CC312 OC311 9 0.00 4.97896 2
> OC311 CC322 CC312 OC311 9 0.00 10.79472 3
> HCP1 OC311 CC322 CC312 9 0.00 1.46440 1
> HCP1 OC311 CC322 CC312 9 0.00 1.54808 2
> HCP1 OC311 CC322 CC312 9 180.00 0.79496 3
> HCA1 CC312 OC311 HCP1 9 0.00 0.75312 3
>
> [ dihedraltypes ]
>
> [ cmaptypes ]
itp_mol_01.itp:
> ;
>
> [ moleculetype ]
> ; Name nrexcl
> GLY 3
>
> [ atoms ]
> ; 14 atoms
> 1 CC322 1 GLY C1 1 0.0500 12.0110
> 2 HCA2 1 GLY H11 2 0.0900 1.0080
> 3 HCA2 1 GLY H12 3 0.0900 1.0080
> 4 OC311 1 GLY O1 4 -0.6500 15.9994
> 5 HCP1 1 GLY HO1 5 0.4200 1.0080
> 6 CC312 1 GLY C2 6 0.1400 12.0110
> 7 HCA1 1 GLY H2 7 0.0900 1.0080
> 8 OC311 1 GLY O2 8 -0.6500 15.9994
> 9 HCP1 1 GLY HO2 9 0.4200 1.0080
> 10 CC322 1 GLY C3 10 0.0500 12.0110
> 11 HCA2 1 GLY H31 11 0.0900 1.0080
> 12 HCA2 1 GLY H32 12 0.0900 1.0080
> 13 OC311 1 GLY O3 13 -0.6500 15.9994
> 14 HCP1 1 GLY HO3 14 0.4200 1.0080
>
> [ bonds ]
> ; 13 bonds
> 1 4 1
> 1 2 1
> 1 3 1
> 1 6 1
> 4 5 1
> 6 7 1
> 6 8 1
> 6 10 1
> 8 9 1
> 10 11 1
> 10 13 1
> 10 12 1
> 13 14 1
>
> [ pairs ]
> ; 27 pairs
> 1 9 1
> 1 11 1
> 1 13 1
> 1 12 1
> 2 5 1
> 2 7 1
> 2 8 1
> 2 10 1
> 3 5 1
> 3 7 1
> 3 8 1
> 3 10 1
> 4 7 1
> 4 8 1
> 4 10 1
> 5 6 1
> 6 14 1
> 7 9 1
> 7 11 1
> 7 13 1
> 7 12 1
> 8 11 1
> 8 13 1
> 8 12 1
> 9 10 1
> 11 14 1
> 12 14 1
>
> [ angles ]
> ; 21 angles
> 1 6 10 5
> 1 6 8 5
> 1 6 7 5
> 1 4 5 5
> 2 1 6 5
> 2 1 3 5
> 3 1 6 5
> 4 1 6 5
> 4 1 3 5
> 4 1 2 5
> 6 10 12 5
> 6 10 13 5
> 6 10 11 5
> 6 8 9 5
> 7 6 10 5
> 7 6 8 5
> 8 6 10 5
> 10 13 14 5
> 11 10 12 5
> 11 10 13 5
> 13 10 12 5
>
> [ dihedrals ]
> ; 27 dihedrals
> 1 6 8 9 9
> 1 6 10 11 9
> 1 6 10 13 9
> 1 6 10 12 9
> 2 1 4 5 9
> 2 1 6 7 9
> 2 1 6 8 9
> 2 1 6 10 9
> 3 1 4 5 9
> 3 1 6 7 9
> 3 1 6 8 9
> 3 1 6 10 9
> 4 1 6 7 9
> 4 1 6 8 9
> 4 1 6 10 9
> 5 4 1 6 9
> 6 10 13 14 9
> 7 6 8 9 9
> 7 6 10 11 9
> 7 6 10 13 9
> 7 6 10 12 9
> 8 6 10 11 9
> 8 6 10 13 9
> 8 6 10 12 9
> 9 8 6 10 9
> 11 10 13 14 9
> 12 10 13 14 9
>
> [ dihedrals ]
> ; 0 impropers
>
> [ cmap ]
> ; 0 cmaps
>
--
Carlos Navarrro Retamal
Ingeniero en Bioinformática
Estudiante de doctorado en Ciencias Aplicadas, Universidad de Talca, Chile
Centro de Bioinformática y Simulación Molecular(CBSM)
Universidad de Talca
2 Norte 685, Casilla 721, Talca - Chile
Teléfono: 56-71-201 798,
Fax: 56-71-201 561
Email: carlos.navarro87 at gmail.com o cnavarro at utalca.cl
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