AMBER Archive (2008)

Subject: RE: AMBER: reg.dnasaveparm&tcrd

From: balaji nagarajan (balaji_sethu_at_hotmail.com)
Date: Mon Dec 01 2008 - 10:56:44 CST

thank u !
i will do it as you said

From: ross_at_rosswalker.co.uk
To: amber_at_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_at_scripps.edu
[mailto:owner-amber_at_scripps.edu] On Behalf Of balaji nagarajan

Sent: Monday, December 01, 2008 6:06 AM

To: amber_at_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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