AMBER Archive (2006)

Subject: Re: AMBER: Amber8: problem related to antechamber

From: priya priya (priyaanand_27_at_yahoo.co.in)
Date: Tue Oct 17 2006 - 01:49:03 CDT

Dear Sir
 
 if we load single peptoid residues by antechamber and then try to load sequence by leap, leap window closes automatically ant the terminal giver a error.
 
 Regards

"David A. Case" <case_at_scripps.edu> wrote: On Mon, Oct 16, 2006, priya priya wrote:
>
> When I use antechamber to load a peptoid sequence
> (peptoids have the amino acid side chain appended to
> amide nitrogen ratther then alpha carbon) containing
> charged residues (like lysine). it says "ODD NUMBER OF
> ELECTRONS"....Check!
>
> There are three lysine residues and the total number of electrons come out
> to be 834 but antechamber is taking 837 number of electrons (not
> considering the +3 charge of the three lysine residues.

You have to explicitly tell antechamber the net charge using the "-nc" flag.
The default is zero.

Note also that antehcamber is designed to handle a *single* residue at a time,
not multiple residules as you seem to be trying.

...good luck...dac

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

                                 
---------------------------------
 Find out what India is talking about on - Yahoo! Answers India
 Send FREE SMS to your friend's mobile from Yahoo! Messenger Version 8. Get it NOW
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu