[gmx-users] OPLS-AA nonbonded force field format

[Justin Lemkul]

On 1/31/17 8:16 PM, Shi Li wrote:
> Dear GMX users,
>
> I am editing an OPLS-AA non-bonded itp file for my simulation system. I
> noticed in the ffoplsaa in gromacs folder, the non-bonded force field has
> following format:
>
> [ atomtypes ] ; full atom descriptions are available in ffoplsaa.atp ; name
> bond_type    mass    charge   ptype          sigma      epsilon opls_001   C
> 6      12.01100     0.500       A    3.75000e-01  4.39320e-01 ; SIG …
>
> However, the non-bonded format I find from the manual is like this:
>
> [ atomtypes ] ;name at.num mass charge ptype V(c6) W(c12) O 8 15.99940 0.000
> A 0.22617E-02 0.74158E-06 OM 8 15.99940 0.000 A 0.22617E-02 0.74158E-06
>
> The difference is in the manual, it doesn’t contain the first column, which I
> think is the atom name. When I built my own non bonded itp file, I try make
> my file looks like the first one. For example, if I have an atom name S1, and
> belongs to type “S”, my first line of the file looks like this: [ atomtypes
> ] ; full atom descriptions are available in ffoplsaa.atp ; name  bond_type
> mass    charge   ptype          sigma      epsilon ;   S1    S      16
> 32.0600     0.266702   A  0.3550    1.046700
>
> However, this give me the error as followings: Fatal error: Atomtype S not
> found
>
> This could be fixed if I remove the S1 column and make my file format likes
> the one in the manual. So, my question is, what is the correct non-bonded
> forcefield format for OPLS? If I don't specify the name of the atoms, I think
> they are specified in the topology file, under the [ atoms ], is that
> correct? In this case, how should the first format work in the grompp?
>

Atom *names* never appear in the ff*bonded.itp files.  These are all atom 
*types* because names are irrelevant from the perspective of the force field. 
OPLS is a bit funny because it uses bonded and nonbonded types.  There are far 
fewer bonded types and parameters are shared among multiple nonbonded types.

So column 1 is the nonbonded type, and column 2 is the bonded type (you will 
note that there's nothing that says "opls_" in ffbonded.itp).

> Another question about this non-bonded file is, I think I just need to
> specify the atom types, instead of every single atom in my molecule, is this
> correct? As I tried to include all the atoms in the nonbonded file, but it
> will give me the warning of override the atoms. But the format in opls seems
> to have all the atoms listed. In this case, how should I edit the non-bonded
> file correctly?
>

Parameters need to be uniquely defined.  You don't need to have an entry for 
every atom in the structure, because likely some types are the same.

-Justin

-- 
==================================================

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
http://mackerell.umaryland.edu/~jalemkul

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