AMBER Archive (2006)

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

From: Dave, Sonya (
Date: Fri Nov 03 2006 - 11:54:06 CST


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 PMEMD.
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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