[gmx-users] defining hydrogen bond donars and acceptors
SLN Prasad Reddy
sreeyapu at rediffmail.com
Sat Sep 4 07:33:25 CEST 2004
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I am very happy to inform you that i am successful in geting hydrogen bonds between protein and ATP. But it was possible only because your suggestion. I am really greatful for your help.
Thanking you once more
On Sat, 28 Aug 2004 David wrote :
>On Sat, 2004-08-28 at 11:50, SLN Prasad Reddy wrote:
> > Hello gromacs usres,
> > To simulate my protein with ATP i am using force field no:2 of gromacs version 3.1.1. When i tried to analyse hydrogen bonds between protein and ATP , program complaining that there are no donors and acceptors in a group "ATP" . Kindly let me know how and where to define acceptors and donors in ATP. I changed atom names of ATP present in ffG---.rtp file.
> > Many thanks in advance
>you probably have te remove the A for all the atom names, make a new
>topology and retry.
> > prasad reddy.
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>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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