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SLN Prasad Reddy sreeyapu at rediffmail.com
Sat Aug 28 11:16:29 CEST 2004

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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. 

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 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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