[gmx-users] gromacs.org_gmx-users Digest, Acetonitrile with CHARMM ff

Sonia Milena Aguilera Segura sonia-milena.aguilera-segura at enscm.fr
Wed Jul 5 16:48:04 CEST 2017

> On 7/5/17 5:15 AM, Sonia Milena Aguilera Segura wrote:
> > Dear GROMACS users,
> > 
> > I am currently interested in studying properties of some solvents, among
> > them acetonitrile and isopropanol. I would like to use CHARMM force field
> > for compatibility with other molecules and I am taking my initial
> > structure files from virtualchemistry.org. Does someone know how to run
> > the 6-sites model available with the CHARMM ff in gromacs? As I try to run
> > the simulation box I get the error "No Defaul Proper Dih. Types". I
> > checked the ffbonded file and I didn't see the dihedrals defined as in the
> > rtp file. And for what I've understood this is
> Dihedrals aren't required in .rtp files since pdb2gmx generates them.

Dear Justin, 

Thank you for the comments. Yes, sorry, I was referring to the top file generated by pdb2gmx instead of the rtp file. The top file has the dihedrals defined whereas ffbonded files does not.  

> because acetonitrile is a linear molecule and dihedrals for three colinear
> atoms
> this are mathematically
> There are still H-C-C-N dihedral terms.

Yes, they are named in the top file but not really defined in the ffbonded file, which is why I get the error. 

> undefined. Also, when I go to check the available itp for acetonitrile in
> virtualchemistry.org, I can see that there is a 7-sites model,with a dummy
> atom
> included. However, for this case, pdb and itp files do not match. I have seen
> that this can be sort of solved by fixing the angle as 179.9, but I really
> don't
> exactly what to change
> >    or where in the force field files. I have no experience modifying force
> >    fields. Also, I've seen that for
> Don't modify the force field.  The CHARMM parameters for acetonitrile were
> generated in CHARMM, which can handle linear angles without the tricks that
> GROMACS requires with virtual sites.

So, what you are saying is that it is not possible to simulate the 6-sites model of acetonitrile in GROMACS using CHARMM? 

> the opls ff both pdb and itp files match, but I really need to use the CHARMM
> force field. Are the opls parameters compatible with CHARMM? Any advice?
> > 
> Don't mix and match force fields.

Then, if I cannot run the 6-sites model, what's the advice? I would really need to run acetonitrile with CHARMM, because I have other series of molecules such as cellulose and other saccharides. In that case, what would be the most compatible for field to simulate organic solvents and saccharides?  

> > Also, I cannot find an already optimized structure with all hydrogens for
> > isopropanol. Could somenone provide one?
> Take any valine side chain and use it.  You can generate any missing H easily
> with a suitable .hdb entry.
> -Justin

Thank you for your advice, 

Sonia Aguilera
PhD student

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