Re: AMBER: hbond ptraj pls help.

From: Catein Catherine <>
Date: Wed, 23 May 2007 18:17:27 +0800

Dear Kateryna,

Thank you very much for your help. I got it works now, but in some of the
specification, i found an error message like this, is it just normal or need
to be fixed?

best regards,


>From: Kateryna Miroshnychenko <>
>Subject: Re: AMBER: hbond ptraj pls help.
>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
> > 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
>The AMBER Mail Reflector
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Received on Sun May 27 2007 - 06:07:06 PDT
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