Re: AMBER: hbond ptraj pls help.

From: Kateryna Miroshnychenko <>
Date: Wed, 23 May 2007 12:01:03 +0300

Dear Catherine,

You have missed word mask and : before residue number.
Try following (see p.262 in amber9 manual)
donor mask :610.O
donor mask :610.N
acceptor mask :720.N :720.HN
[the name of the hydrogen attached to the N is HN, I suppose?]
> Dear Sir/Madam,
> I could like to do the analysis for the hbond bonds between residues LYS610
> and SER720 only, but not all the LYS and SER in the PDB file. Could you
> mind to let me know what is the right approach to write the ptraj file?
> I tried :
> donor 610.O
> donor 610.N
> acceptor 720.N 720.NH

 Kateryna Miroshnychenko
post-graduate student
Department of Biological Physics,
Institute of Radiophysics and Electronics,
National Academy of Sciences of Ukraine,
12, Proskura st., Kharkiv, 61085, Ukraine

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Received on Sun May 27 2007 - 06:07:05 PDT
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