[gmx-users] OPLSAA parameters

Elisabeth katesedate at gmail.com
Mon Aug 1 01:42:28 CEST 2011 

Thanks Justin for your guidance. By following your tips, I have now all the
parameters I need... Please let me know if I am missing any [ angletypes ]
or [ dihedraltypes ] for a hydrocarbon molecule.

Best,

[ bondtypes ]
;  i     j     func     b0       kb
  CT    CT      1    0.15290   224262.4   ; CHARMM 22 parameter file
  CT    HC      1    0.10900   284512.0   ; CHARMM 22 parameter file

[ angletypes ]
;i      j     k      func   th0       cth
CT     CT     CT      1   112.700    488.273   ; CHARMM 22 parameter file
CT     CT     HC      1   110.700    313.800   ; CHARMM 22 parameter file
HC     CT     HC      1   107.800    276.144   ; CHARMM 22 parameter file

[ dihedraltypes ]
  CT     CT     CT     CT      3      2.92880  -1.46440   0.20920
-1.67360   0.00000   0.00000 ; hydrocarbon all-atom
  CT     CT     CT     HC      3      0.62760   1.88280   0.00000
-2.51040   0.00000   0.00000 ; hydrocarbon all-atom
  HC     CT     CT     HC      3      0.62760   1.88280   0.00000
-2.51040   0.00000   0.00000 ; hydrocarbon *new* 11/99





On 30 July 2011 07:40, Justin A. Lemkul <jalemkul at vt.edu> wrote:

>
>
> Elisabeth wrote:
>
>> Hello to all,
>>
>> I am looking for bonded and nonbonded parameters for C H atoms in
>> saturated hydrocarbons.
>>
>> atom types are:
>> Carbon atoms opls_135      opls_136     H  opls_140
>>  opls_135   12.01100  ; alkane CH3
>>  opls_136   12.01100  ; alkane CH2
>>  opls_140    1.00800  ; alkane H.
>>
>> Please help me out with the following:
>>
>> - I am wondering if I am selecting the correct values, for C-C and C-H
>> bonds from ffoplsaabon.itp.
>>
>>
> The C-C bond is not correct for alkanes.  It is for the C-C bond of oxalic
> acid, as the comment indicates.  In ffnonbonded.itp, you can see how opls_*
> types are mapped to different bonded atom types (for instance, opls_135/136
> are CT).  Note that in the topology, you do not have to explicitly define
> values when using OPLS-AA; any bond between two defined bonded atom types
> will be automatically detected and used.
>
>
>  C     C       1    0.15100   292880.0   ; wlj oxalic acid, etc.
>> HC    C       1    0.10900   284512.0   ; wlj 7/96
>>
>> - what does wlj mean?
>>
>>
> Probably someone's initials, which occur frequently to indicate either the
> source of the parameters or the individual that added them.  In this case,
> my guess would be Jorgensen is the referenced individual here.
>
>  - what are the units?
>>
>>
> This is in the manual.
>
>
>
>> Angle
>>
>>  CA     CA     CZ      1   120.000    585.760   ; wlj
>>  CA     CA     CR      1   120.000    527.184   ;
>>  CA     CA     CX      1   120.000    711.280   ;
>>  C      CT     Cl      1   109.800    577.392   ; wlj
>>
>> - I can not distinguish CA CZ .... What are they referring to?
>>
>>
> See the above tip about converting atom types in ffnonbonded.itp.
>
>
>  [ dihedraltypes ]
>>
>>  C      C      CT     HC      3      0.17782   0.53346   0.00000  -0.71128
>>   0.00000   0.00000 ; dicarbonyls BMC 8,1881(2000)
>>
>> - Is this what I need for oplsaa 135 136 140?
>>
>>
> Probably not.  The comment indicates the dihedral is for dicarbonyls.  The
> appropriate dihedral is:
>
>  CT     CT     CT     HC      3      0.62760   1.88280   0.00000  -2.51040
> 0.00000   0.00000 ; hydrocarbon all-atom
>
> Note how the comment indicates it is for use with hydrocarbons.  Again,
> like bonds as described above, you do not need to explicitly list parameters
> in the topology.  They will be inferred from the atom types.
>
>
>  ffoplsaanb.itp.
>>
>>  opls_135   CT    6     12.01100    -0.180       A    3.50000e-01
>>  2.76144e-01
>>  opls_136   CT    6     12.01100    -0.120       A    3.50000e-01
>>  2.76144e-01
>>
>>  opls_140   HC    1      1.00800     0.060       A    2.50000e-01
>>  1.25520e-01
>>
>> - are these parameters for
>>
>>  opls_135   12.01100  ; alkane CH3
>>  opls_136   12.01100  ; alkane CH2
>>  opls_140    1.00800  ; alkane H.
>>
>> ?
>>
>>
> Yes.
>
>
>  Also in usr/local/gromacs/share/**gromacs/top/ directory  I can not find
>> ffoplsaanb,itp and ffoplsaabon.itp for 4.5.4 whereas in previous versions
>> these files were accessible. I am using itp files from version 4.0.7 and
>> wanted to make sure the above parameters for oplsa_135 oplsa_136 and
>> oplsa_140 have been remained unchanged in 4.5.4. Where can I find these
>> files?
>>
>>
> The force field organization has changed, but the content of the force
> fields has not.  This is described in the manual.  All the equivalent files
> are now in the oplsaa.ff subdirectory.  For backwards compatibility, the
> statement #include "ffoplsaa.itp" will indeed call the force field, because
> you will note that ffoplsaa.itp now simply calls the correct force field
> with #include "oplsaa.ff/forcefield.itp."
>
> -Justin
>
> --
> ==============================**==========
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>
> ==============================**==========
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