[gmx-users] Help with topology file

[David]

On Thu, 2003-03-20 at 19:50, Alexandre Suman de Araujo wrote:
> Hi Gmxers
> 
> I'm building a topology file using oplsaa force fields parameters. I 
> used the atoms type from ffoplsaa.atp, then the begining of my topology 
> file is like this:
> 
>  [ atoms ]
>  ;  nr  type resnr resid  atom  cgnr charge
>      1  opls_140 1 DRG     H20     1    0.000
>      2  opls_140 1 DRG     H21     2    0.000
>      3  opls_140 1 DRG     H22     3    0.000
>      4  opls_135 1 DRG     C60     4    0.000
> ... and it goes on...
> 
> Well, my question is: I need, in my topology file, of the sessions 
> [bond], [angles], etc??? Or these parameters is automatically got from 
> ffoplsaabon.itp, since I put #include "ffoplsaa.itp" statment in my 
> topology file?
> Thanks for the help and waiting answers.
If the topology is correct you need only modify the atomtypes, and the
OPLS stuff will work. However OPLS is slightly different than GROMOS:

you will have to specify *all* possible dihedrals and 1-4 interactions
(and set nrexcl = 3)

> 
> 
> -- 
> Alexandre Suman de Araujo
> asaraujo at if.sc.usp.br
> UIN: 6194055
> IFSC - USP - São Carlos - Brasil
> 
> 
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-- 
Groeten, David.
________________________________________________________________________
Dr. David van der Spoel, 	Dept. of Cell and Molecular Biology
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
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