[gmx-users] Energy Calculation

[David]

On Fri, 2004-06-25 at 08:10, Gaurav Porwal wrote:
> Hi,
> 
> When I'm trying to calculate the energy of a predicted structure of an 85
> residue protein, i'm getting the following error by pdb2gmx and all the
> subsequent commands fail (run via a shell script):
> 
> Fatal error: Incomplete ring in HIS68
And have you checked whether this is correct?

pdb2gmx can only treat "normal" proteins, so if you're missing atoms
it's a problem.
> 
> Is there a way in which I can calculate/minimize this energy. I've tried
> using -missing flag in pdb2gmx but that doesn't work. Plz. help.
> 
> Thanks in advance.
> 
> Regards,
> Gaurav
> 
> **********************************************************************
> It's amazing what a man can accomplish when he's not worried about who
> will get the credit.
> **********************************************************************
> 
>                            Gaurav Porwal
> 		    Senior Undergraduate Student
> 		  Department of Chemical Engineering
>                          IIT Bombay, Powai
>                           Mumbai - 400076
>                               INDIA   
>                           Ph. - 9869277620
> 
> Alternative Email Id's :-
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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://xray.bmc.uu.se/~spoel
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