Re: AMBER: Thermodynamic Integration with Explicit Solvent

From: Thomas Steinbrecher <>
Date: Tue, 9 Oct 2007 17:12:13 -0700 (PDT)

Hi Scott,

the error you mention indicates that your prmtop is set for a trucated
octahedron solvent box, while your rst file is for a rectangular
box. Check its last line, the 4th-6th number, indictaing the box angles,
should be 90.0 degrees for a rectangular and 109.47 for an octahedral
box. Why you only get this error in a TI run is strange however, it should
occur in regular MD, too.

Kind Regards,


Dr. Thomas Steinbrecher
The Scripps Research Institute
10550 N. Torrey Pines Rd.
San Diego CA 92037, USA

On Tue, 9 Oct 2007, Scott Pendley wrote:

> Hello AMBER users,
> I have had a long history of using thermodynamic integration under AMBER 7
> using parmtops and perturbed parmtops. I have read through Ross' AMBER 9
> tutorial and I am trying to modify his implicit solvent tutorial to handle
> my explicit solvent needs but I am having trouble getting it to work.
> First I attempted to using an TI input that worked well for me before with
> &cntrl
> ntr=0,
> nstlim=3000000, nscm=2000, ntave=5000,
> ntx=7, irest=1, ntb=1, ntpr=100,
> ntp=0, taup=2.0,
> dt=0.001, nrespa=2,
> ntt=0, temp0 = 300., tautp=2.0,
> ntc=2, ntf=2, tol=0.000001,
> ntwr = 10000, ntwx=0, klambda=6,
> icfe=1, clambda=0.043882786,
> cut=9.0,
> /
> This unfortunately, led to errors with values exceeding the vmax. Next I
> tried to modify Ross' input to allow for explicit solvent and am using
> &cntrl
> nstlim =3000000, nscm=2000,
> ntx=1, irest=0, ntpr=1000,
> tempi=300.0, temp0=300.0, ntt=3, gamma_ln=5.0,
> ntb=0, igb=0, cut=9.0,
> dt=0.001,
> ntc=2, ntf=2,
> ntwr = 10000, ntwx=1000, ntave=5000
> icfe=1, clambda=0.0034357, klambda=6,
> /
> This leads to a very strange error "Error: ifbox=2 in prmtop but angles are
> not correct". I have tried the parmtop and coordinate files with a regular
> MD input and they seem fine. If others have had success could they share
> their input file with me or any suggestions that can help me further along
> this way.
> Thank you,
> Scott
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Received on Wed Oct 10 2007 - 06:07:56 PDT
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