[gmx-users] surfactant.itp file

[Justin Lemkul]

On 11/18/15 3:56 AM, mahdiyeh poorsargol wrote:
> Hello
> I'm a beginner in Gromacs and I want to work with the surfactant (for
> example SDS surfactant). I converted the surfactant.pdb file to the
> surfactant.itp file using TOPOLGEN, but for S atom, atomtype not
> defined!
> please help me. thankyou
>

A simple Google search for "OPLS-AA SDS" turns up numerous papers that have done 
simulations with OPLS models for SDS.  Start there rather than reinventing the 
wheel.

TopolGen is unlikely to succeed here because the parameters it uses are 
generally referenced from standard groups in the protein force field, so support 
for sulfates, etc. will be limited.

-Justin

> [ atoms ]
> ;   nr       type  resnr residue  atom   cgnr     charge       mass
> typeB    chargeB      massB
> .
> .
>     30   opls_136      1     LIG      C     10     -0.120   12.01100
>      31   opls_140      1    LIG      H     10      0.060    1.00800
>      32   opls_140      1    LIG      H     10      0.060    1.00800
>      33   opls_136      1    LIG      C     11     -0.120   12.01100
>      34   opls_140      1    LIG      H     11      0.060    1.00800
>      35   opls_140      1    LIG      H     11      0.060    1.00800
>      36   opls_136      1    LIG      C     12     -0.120   12.01100
>      37   opls_140      1    LIG      H     12      0.060    1.00800
>      38   opls_140      1    LIG      H     12      0.060    1.00800
>      39          1           0      S       12      32     0.000
> 0.00000
>      40   opls_236      1    LIG      O     12     -0.500   15.99940
>      41   opls_154      1    LIG      O     12     -0.683   15.99940
>      42   opls_155      1    LIG      H     12      0.418    1.00800
>

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

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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