[gmx-users] (no subject)

[David]

On Sat, 2004-08-28 at 11:16, SLN Prasad Reddy wrote:
>   
> Dear Xavier Periole,
>          thanks for your mail. I used grep command to find out the term 'donors' on all the corrosponding files of force field i am using. I am using ff-2 of Gromacs version 3.1.1. But no file is having term 'donor'. Kindly suugest me any other way to over come this problem. 
> 
There is no information on donors or acceptors. g_hbond just uses the
atom names, O and N for acceptors, and you need H for donors connected
to O or N. 


> Thanking you
> 
> prasad reddy. 
> 
> On Fri, 27 Aug 2004 Xavier Periole wrote :
> >SLN Prasad Reddy wrote:
> >
> >>  Hello gromacs users,
> >>          I am working on  a protein with ATP. When i do hydrogen bond anlysis (g-hbond), gromacs is complaining 
> >>No Donors or Acceptors found in group 'ATP'
> >>
> >>    i used PDB file of ATP containing all residues as per *.rtp file.
> >>
> >>Kindly suggest me a solution for my problem.
> >>
> >>Many thanks in advance
> >>
> >>prasad reddy 
> >>  
> >You have to define the donors and acceptors atoms some where in the toplogy files !!!
> >Probably not done for ATP !! A grep on donor on all the files in the top directory
> >should help you find out how to define those donor/acceptor
> >XAvier
> >
> >-- ----------------------------------------------
> >
> >   Xavier Periole - Ph.D.
> >
> >   Dept. of Biophysical Chemistry / MD Group   Univ. of Groningen
> >   Nijenborgh 4
> >   9747 AG Groningen
> >   The Netherlands
> >
> >   Tel: +31-503634329
> >   Fax: +31-503634800
> >   email: x.periole at chem.rug.nl
> >   web-page: http://md.chem.rug.nl/~periole
> >   ----------------------------------------------
> >
> >
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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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