[gmx-users] gromacs.org_gmx-users Digest, Acetonitrile with CHARMM ff
jalemkul at vt.edu
Wed Jul 5 23:47:17 CEST 2017
On 7/5/17 10:47 AM, Sonia Milena Aguilera Segura wrote:
>> 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
>> 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.
pdb2gmx will blindly generate all possible dihedrals; sometimes this isn't right.
It even appears that such parameters (H-C-C-N) do not exist in any CHARMM force
field file. Perhaps it's meant that way, but I have never tried to simulate
anything with it.
>> 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
>> 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
>> 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?
Never tried it. AFAIK, GROMACS needs special treatment for linear species.
Hopefully someone who has actually done such a simulation will say something,
because my usefulness here is at its end :)
>> 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.
> Thank you for your advice,
> Sonia Aguilera
> PhD student
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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