Dear Justin,
Thank you for your reply. I went trough the CHARMM forum and I found this post
of 2007,
https://www.charmm.org/ubbthreads/ubbthreads.php?ubb=showflat&Number=28545,
which basically underlines the same issues I am having. I read this post before
posting here, and this why I came with the idea of modifying the dihedral ff
parameters, as suggested in the forum. Apparently, it may work if I set the
amplitude k=0 and I distort the linear angle a little (maybe 179.9) in the
initial structure. The thing is, as I say before, I have no experience
modifying force fields, so I wouldn't what to put and where. My guess is that I
would need to go the ffbonded.itp file and modify and add the following lines
in this way:
[ angletypes ]
; i j k func theta0 ktheta ub0
kub
CG331 CG1N1 NG1T1 5 179.900000 177.401600 0.00000000
0.00
[ dihedraltypes ]
; i j k l func phi0 kphi mult
HGA3 CG331 CG1N1 NG1T1 9 0.000000 0.000000 1
[ dihedraltypes ]
; 'improper' dihedrals
; i j k l func phi0 kphi
HGA3 CG331 CG1N1 NG1T1 9 0.000000 0.000000 1
Please let me know if this makes any sense. Is it correct to modify the
angletype or should I only modify the initial structure?
Is there someone who has already done simulations with acetonitrile? Any advice
and feedback is very much welcome!!
Thank you very much,
Have a nice day,
Sonia Aguilera
PhD Student
ENSCM
>
> Message: 2
> Date: Wed, 5 Jul 2017 17:47:08 -0400
> From: Justin Lemkul <jalem...@vt.edu>
> To: gmx-us...@gromacs.org
> Subject: Re: [gmx-users] gromacs.org_gmx-users Digest, Acetonitrile
> with CHARMM ff
> Message-ID: <c935a574-ffc8-cf5f-3a3c-3131d906a...@vt.edu>
> Content-Type: text/plain; charset=utf-8; format=flowed
>
>
>
> 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
> >> 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.
> >
>
> 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
> >> 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?
>
> 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 :)
>
> -Justin
>
> >
> >>
> >> 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
> > ENSCM
> >
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