[gmx-users] Help with topology file

[David van der Spoel]

On Fri, 2003-03-21 at 15:42, Alexandre Suman de Araujo wrote:
> David van der Spoel wrote:
> 
> >On Fri, 2003-03-21 at 15:18, Alexandre Suman de Araujo wrote: David
> >wrote:
> >            
> >Then I don't need to have [bonds] and [angles] session and I can erase
> >them from the file??? Or the information from ffoplsaa.* files will
> >overwrite the information in the topology file??? 
> >The definition of the atomtypes that you are talking is what I showed in
> >my first msg, didn't it???
> >This possible dihedrals I think was specified automatically by PRODRG...
> >but I'll check them again
> >
> >Yes you do need all that. You got that from prodrg didn't you?
> >
> >
> >Thanks for your answer.
> >
> >
> >
> >  
> >
> Yes... I got from PRODRG and changed the atomtypes from ffgmx to 
> ffoplsaa. I didn't understand if I can keep the [bonds] and [angles] 
> sessions, created by PRODRG and with different values for oplsaa(they 
> are correct to ffgmx, of course), in my topology file them gromacs 
> overwrite their values for the correct ones or if I need to erase them 
> and gromacs will get the values from ffoplsaa.* file???
you need the defintions of bonds etc.
[ bonds ]

1 2
2 3
3 4

more than that you don't need. 

> Thankyou very much for the help.
> 
> -- 
> 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 & Mol. 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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