AMBER Archive (2006)

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

From: Carlos Simmerling (carlos_at_csb.sunysb.edu)
Date: Fri Nov 03 2006 - 12:05:22 CST

when you use a minimization restart file as input to MD, you
can't read velocities since there are none in the min output.
you should set ntx=1 and irest=0 when reading a min restart file.
Since you don't give your md input file I can't say for sure
but that is probably the error.
carlos

Dave, Sonya wrote:

>
> Hi,
>
> 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 min1.in
> -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
> &cntrl
> imin=1, maxcyc=1000, ncyc=500,
> cut=999., rgbmax=999.,igb=1, ntb=0,
> ntpr=100
> /
>
> Then, I run a molecular dynamics command: mpiexec -np 2
> $AMBERHOME/exe/sander -O -i heat1.in -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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