[gmx-users] Acetonitrile and isopropanol with CHARMM ff

Justin Lemkul jalemkul at vt.edu
Wed Jul 5 15:04:47 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.

because acetonitrile is a linear molecule and dihedrals for three colinear atoms 
this are mathematically

There are still H-C-C-N dihedral terms.

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.

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.

> 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 A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


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