[gmx-users] Atomtype OW not found - spc water model

[Carlos Navarrro Retamal]

Hi Justin,
Thanks for the advice.
I solved my problem by just including the charmm27.ff forcefield itself at the top of the topol.top file (and deleting the default line)
I guess that with this change i’m adding the atomtype OW into the topology file.
I’m going to follow your advices respect to what water model should i use.
Cheers,


--  
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


On Tuesday, April 8, 2014 at 4:30 PM, Justin Lemkul wrote:

>  
>  
> On 4/8/14, 11:18 AM, Carlos Navarrro Retamal wrote:
> > 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.
> >  
>  
>  
> In theory, the CHARMM27 files that come with Gromacs can support SPC, but in  
> practice, there is no reason for you to do it. CHARMM force fields are  
> parametrized for use with TIP3P; other water models risk invalidating the force  
> field.
>  
> -Justin
>  
> --  
> ==================================================
>  
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>  
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 601
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>  
> jalemkul at outerbanks.umaryland.edu (mailto:jalemkul at outerbanks.umaryland.edu) | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>  
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