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.navarr...@gmail.com o cnava...@utalca.cl -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? 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