[gmx-users] surfactant.itp file

[Justin Lemkul]

Please do not incessantly post the same question. I provided a suggestion 
yesterday for how to deal with that. If you want free help, you have to 
contribute by demonstrating a willingness to respond to suggestions.

-Justin

On 11/19/15 6:27 AM, mahdiyeh poorsargol wrote:
> ---------- Forwarded message ----------
> From: mahdiyeh poorsargol <poorsargol.m64 at gmail.com>
> Date: Thu, 19 Nov 2015 14:56:55 +0330
> Subject:
> To: gmx-users <gmx-users at gromacs.org>
>
> 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
>
> [ 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
>
> I have a OPLS-AA SDS, but I don't know how include in the TOPOLGEN!
> I use the command line: perl topolgen.pl -f input.pdb -o output.itp -type itp
> please help me!
>

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

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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