Hi Balaji,
>From what you post I see no errors, just warnings. You should be safe to
ignore these. It is basically saying that your waters are missing head and
tail atoms, which is correct since they don't form part of the protein
chain. Check that you have a prmtop and inpcrd file. You should visualize
this in something like VMD to make sure it looks okay, the bonding looks
good etc.
All the best
Ross
From: owner-amber.scripps.edu [mailto:owner-amber.scripps.edu] On Behalf Of
balaji nagarajan
Sent: Monday, December 01, 2008 6:06 AM
To: amber.scripps.edu
Subject: AMBER: reg.dnasaveparm&tcrd
hai !
greetings to everyone
I am a new user of AMBER , time being I am running a dna dynamics ,
i have a problem in saving top and crd files after putting water box to my
case
its giving out some error
aveamberparm model2 polyAT_wat.prmtop polyAT_wat.inpcrd
Checking Unit.
Building topology.
Building atom parameters.
Building bond parameters.
Building angle parameters.
Building proper torsion parameters.
Building improper torsion parameters.
total 240 improper torsions applied
Building H-Bond parameters.
Not Marking per-residue atom chain types.
Marking per-residue atom chain types.
(Residues lacking connect0/connect1 -
these don't have chain types marked:
res total affected
WAT 5108
)
(no restraints)
is it actually a error !
while i do minimization its working
thanks in advance !
_____
It is a cricketing clash meant for the Gods! Be there when we track the T-20
Champions League this December Try <
http://sports.in.msn.com/> it now!
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Received on Fri Dec 05 2008 - 18:22:41 PST
