AMBER Archive (2007)

Subject: Re: AMBER: hbond ptraj pls help.

From: Catein Catherine (askamber23_at_hotmail.com)
Date: Wed May 23 2007 - 05:17:27 CDT

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,

Cat.

>From: Kateryna Miroshnychenko <kateryna_mirosh_at_ire.kharkov.ua>
>Reply-To: amber_at_scripps.edu
>To: amber_at_scripps.edu
>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_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
>********************************************
>
>-----------------------------------------------------------------------
>The AMBER Mail Reflector
>To post, send mail to amber_at_scripps.edu
>To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu

_________________________________________________________________
Learn English via Shopping Game, FREE!
http://www.linguaphonenet.com/BannerTrack.asp?EMSCode=MSN06-03ETFJ-0211E

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu