Re: DNA Tutorial Script

From: Holger Gohlke <>
Date: Wed 04 Sep 2002 20:29:23 -0700

Dear Joel,

I had a look into the first two sander calculations, i.e. the ones with and in Run.equil.

You have to make the following changes:
1. In atA.coords, add as the last line in the file the box coordinates:
"61.317974 41.857475 41.857475 90.0000000 90.0000000 90.0000000"

2. In, add "ntp = 1," to the &cntrl namelist.

3. In, remove "ndfmin = 0, init = 3, tauts = 0.2, nrun
= 1" from the name list and add "nmropt = 1".

This equilibration part still "suffers" from going from amber6 to
amber7, I'm currently testing the following simulations in Run.equil.
Thank you for reporting the problem.

Best regards


> When running the Run.equil script found in the DNA tutorial
> <>,
> I get the following error message.
> ----------------------
> $ Run.equil sander
> Arithmetic Exception
> FAILED. Sorry bud.
> ----------------------
> I've downloaded all the input files. What's going on?
> -Joel

Dr. Holger Gohlke
Dept. of Molecular Biology, TPC15
The Scripps Research Institute
10550 N. Torrey Pines Rd.
La Jolla CA 92037  USA
phone: +1-858-784-9788
fax:   +1-858-784-8896
From 5 Sep 2002 17:16:03 -0000
Message-id: <>
Date: 5 Sep 2002 17:16:03 -0000
From: Raja  Swaminathan <>
To: AMBER list <>
Subject: average structure
In-Reply-to: <>
I have done a 2ns MD on an unusual DNA duplex. for average 
structure analysis i have used the following inputs
this is the first one
/home/programs/amber6/exe/ptraj << EOF
trajin dat6_nowat_final.stripped.Z (without any water or ions)
average average2ns.pdb pdb
second is
/home/programs/amber6/exe/ptraj << EOF
trajin dat6_nowat_final.stripped.Z
center :1-14 mass origin
image origin center
center :1-28 mass origin
image origin center
average average2ns_1.pdb pdb
in both the cases i have used the imaged file as inputs. in both 
the cases i get two different pdb coordinates. rms between the two 
structure varies by about 0.7 A.
why it is so. in both the cases i am using the same inputs, if i 
try to image once again the stripped files i am facing this 
Thanking u in advance
Raja Swaminathan
Received on Wed Sep 04 2002 - 20:29:23 PDT
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