From: Ross Walker <>
Date: Fri, 19 Jan 2007 12:47:24 -0800

Dear Steve,
One possibility:

 &wt type='REST', istep1=0, istep2=5, value1=1.0,
          value2=1.0, &end
&wt='END' &end

You don't have a space before the last &wt so it may be stuck looking for
another namelist. Although this should typically give an error rather than
just hang.
I assume you are running the single processor version of sander? If not then
I suggest you switch to this first as sometimes parallel runs can hang and
error messages get lost that when run in serial mode are written to standard
A couple of other notes regarding your input file.
heat = 0.0,
This is a retired option so you should probably remove it.
You have ntb=0 and ntp=0 but you still specify values for Pres0 and comp -
these shouldn't matter but it probably a good idea to remove them.
Similarly you have shake turned off (ntc=1) but you still specify a
You also have lastrst = 8000000. I would avoid specifying anything here
unless you encounter problems. If you are using amber9 then you certainly
should need it (I think).
All the best

|\oss Walker

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From: [] On Behalf Of
Steve Seibold
Sent: Friday, January 19, 2007 11:54
Subject: AMBER:

Hi Amber

I am trying to run MD with distance restraints. However, with the above
input file AMBER "freezes" up at "Resource Use" (see output file). I realize
my nstlim is low, but I was just attempting to get any steps done. I do have
a RST1 file, but I don't believe it is even attempting to read it yet since
I get the same output with and without havimg the RST1 file accessible or


If I remove the restraint namelist info, the MD runs fine. So, I am thinking
it must be in the namelist for the restraints, but I cannot seem to locate
what the problem is. Can someone take a cursory look at my input file to see
if I am doing something obviously incorrect? I would greatly appreciate it.



Thanks, Steve




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Received on Sun Jan 21 2007 - 06:07:42 PST
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