AMBER Archive (2007)

Subject: Re: AMBER: hbond ptraj pls help.

From: Kateryna Miroshnychenko (kateryna_mirosh_at_ire.kharkov.ua)
Date: Wed May 23 2007 - 04:01:03 CDT

Dear Catherine,

You have missed word mask and : before residue number.
Try following (see p.262 in amber9 manual)
donor mask :610_at_O
donor mask :610_at_N
acceptor mask :720_at_N :720_at_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_at_O
> donor 610_at_N
> acceptor 720_at_N 720_at_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
E-mail:kateryna_mirosh_at_ire.kharkov.ua
********************************************

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