[gmx-users] OPLS-AA nonbonded force field format
David van der Spoel
spoel at xray.bmc.uu.se
Wed Feb 1 10:44:36 CET 2017
On 01/02/17 02:50, Justin Lemkul wrote:
> 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 ;
>> 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
>> 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
>> 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: [
>> ] ; full atom descriptions are available in ffoplsaa.atp ; name
>> 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
>> This could be fixed if I remove the S1 column and make my file format
>> 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.
OPLS does this because in many cases the only difference between
atomtypes is the partial charge. Partial charge is a property of the
atom type in other words, unlike most other force fields.
> 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
>> to have all the atoms listed. In this case, how should I edit the
>> 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.
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205.
spoel at xray.bmc.uu.se http://folding.bmc.uu.se
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