[gmx-users] .top file format

[David van der Spoel]

Ashutosh Jogalekar wrote:
> I have a simple question; is the .top file a formatted file?
> I am trying to put in some RB dihedral parameters in the file for an  
> unnatural acid. My question is; does the exact spacing of the lines  
> matter?
> For example, if c0, c1, c2, c3, and c4 are the coefficients for some  
> dihedral combination 1 2 3 and 4, and if W X Y Z are the values of  the 
> parameters which I have to plug in, then:
> 
> 
>                                          c0                          
> c1                             c2                                 c4
> 
> 1 2 3 4                              W                           
> X                               Y                                   Z
> 
> Is this format regarded by GROMACS in the same way as, say,
> 
> 
> 
>                                          c0                          
> c1                             c2                                 c4
> 
> 1 2 3 4    W         X            Y            Z
yes.

you forgot the function type and ryckaert bellemans takes six parameters.

> 
> 
> That is, does the specific spacing matter for the .top file?
no

> Thanks very much
> Ashutosh Jogalekar
> Emory University
> 
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-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
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://folding.bmc.uu.se
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