AMBER Archive (2007)

Subject: Re: AMBER: ambpdb gives empty cpin

From: tri nam Vo (mouseelephant2002_at_yahoo.com)
Date: Tue May 22 2007 - 09:01:42 CDT


Maybe you can check the prmcrd and prmtop file. Is it have titration site such as GL4, AS4, TYR, HIP,...?
dac
bhu <achuthpnr_at_yahoo.co.in> wrote: Dear Sir,
I am usig amber9 and want to do some constant ph
calculations with some polymer molecules. i tried to
create the cpin files as described in the manual using
ambpdb
>>ambpdb -p prmtop < prmcrd | cpinutil.pl > cpin
but i ended up with an empty file also no error
messages are displayed.
the molecule contains no aminoacid residues. the whole
chain is considered to be asingle residue <1>. also it
contains amide bonds.
please help
thank You.

Achu

Office firewalls, cyber cafes, college labs, don't allow you to download CHAT? Click here: http://in.messenger.yahoo.com/webmessengerpromo.php
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu

       
---------------------------------
Yahoo! oneSearch: Finally, mobile search that gives answers, not web links.
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu