AMBER Archive (2008)

Subject: RE: AMBER: reg.dnasaveparm&tcrd

From: Ross Walker (
Date: Mon Dec 01 2008 - 10:44:57 CST

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



From: [] On Behalf Of
balaji nagarajan
Sent: Monday, December 01, 2008 6:06 AM
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
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 !



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Champions League this December Try <> it now!

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