thank u !
i will do it as you said
From: ross.rosswalker.co.uk
To: amber.scripps.edu
Subject: RE: AMBER: reg.dnasaveparm&tcrd
Date: Mon, 1 Dec 2008 08:44:57 -0800
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
it now!
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Received on Fri Dec 05 2008 - 18:22:48 PST
