AMBER Archive (2006)

Subject: RE: AMBER: Simulation a small chain of amino acids - error in MD simulation

From: Dave, Sonya (
Date: Fri Nov 03 2006 - 13:20:55 CST

Thank you for your help. That solved it.


-----Original Message-----
From: on behalf of Ross Walker
Sent: Fri 11/3/2006 12:32 PM
Subject: RE: AMBER: Simulation a small chain of amino acids - error in MD simulation
Hi Sonya,
In your change irest=1 to irest=0 and things should be fine. Also
set ntx=1 if you have it set to something else.
A restart file from a minimisation contains only coordinates since there are
no velocities. Whereas a restart file from MD also contains the velocities.
Thus the procedure you should typically use is:
Minimisation (set irest=0 and ntx=1)
First step of MD from minimised structure (set irest=0 and ntx=1) since this
is not a restart of a previous MD simulation - you just want the coordinates
from the minimisation. In this case the initial velocities (if tempi>0) will
be generated from a Gaussian distribution.
Second and subsequent MD's (set irest=1 and ntx=5). In this case both the
coordinates and velocities from the restart file will be read and the value
of tempi will be ignored.
All the best

|\oss Walker

| HPC Consultant and Staff Scientist |
| San Diego Supercomputer Center |
| Tel: +1 858 822 0854 | EMail:- |
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available on request |

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From: [] On Behalf Of
Dave, Sonya
Sent: Friday, November 03, 2006 09:54
Subject: AMBER: Simulation a small chain of amino acids - error in MD


I am trying to make amber model the structure of a small chain of amino
acids, de novo. I'm following the tutorial on Amber's page (tutorial B3
about TRP cage).

However, I am using my own amino acid sequence, not what was suggested in
the tutorial. Also, I am using ff99SB instead of adjusting ff99. I get an
error in the output file of my first molecular dynamics simulation, which
stops me from doing further simulations.
Here is what I do before the MD simulation:

start leap: $AMBERHOME/exe/tleap -s -f $AMBERHOME/dat/leap/cmd/leaprc.ff99SB
In Leap:
cbs2on2 = sequence {NLYS GLU LEU ARG LEU ILE CGLU}
saveoff cbs2on2 cbs2a2_linear.lib
savepdb cbs2on2 cbs2a2_linear.pdb
saveamberparm cbs2on2 cbs2a2.prmtop cbs2a2.inpcrd

Then I do minimization as follows: $AMBERHOME/exe/sander -O -i -o
min1.out -p cbs2a2.prmtop -c cbs2a2.inpcrd -r min1.rst
This works fine. It also works done with multiple processors, or with
I use the following input file for the above simulation:
Stage 1 - minimisation of TC5b
  imin=1, maxcyc=1000, ncyc=500,
  cut=999., rgbmax=999.,igb=1, ntb=0,

Then, I run a molecular dynamics command: mpiexec -np 2
$AMBERHOME/exe/sander -O -i -p cbs2a2.prmtop -c min1.rst -r
heat1.rst -o heat1.out -x heat1.mdcrd
It says in heat1.out that:

FATAL: Could not read velocities from min1.rst
It does not complete this simulation (but gives no errors at the command
prompt). As such, it gives errors in future MD simulations that use the
results of this MD simulation.

So, does anyone know what I am doing wrong, or what is preventing it from
read ing min1.rst? min1.rst looks like it contains proper information(two
header lines, then six columns of numbers).

Thank you,
Sonya Dave'

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