AMBER: Gibbs pmf calculation

From: Atsutoshi Okabe <okabe.cherry.bio.titech.ac.jp>
Date: Wed, 11 Jan 2006 19:14:30 +0900

Hi, all.

 

I'd like to use Gibbs to calculate free energy varing

 the distance between two molecules.But I always get this

error message in the end of output file.

 

 

Fixed-width window Free Energy Perturbation

 Delta_lambda = 0.0200000; Simulation direction 1->0

                              ------------

                  READING ATOMIC COORDINATES AND VELOCITIES

                  -----------------------------------------

 Title:

ERROR: Restraint read error from RSTIN; Check format:

 23 52

 

 

 

This is the input file I used.

 

&cntrl

 

ntx=1,

ntb=2,

ntp=1,

ntt=5,

dt=0.001,

nstlim=2000,

nstmeq=500,

nstmul=1500,

ntc=2,

ntf=2,

ncorc=1,

cut=8.0,

intprt=1,

ntpr=100,

ntwx=1000,

ntwe=100,

nrun=51,

almda=1.0,

almdel=0.02,

isldyn=-3,

ielper=-1,

intr=1,

scnb=2.0,scee=1.2,

&end

  23 52 0 0 1 0 2 1.00000 0.00000

  10.00000 12.00000 10.00000 2.000000 0 0

 

I checked the format of last two lines in the input file carefully.

But I can't understand why I got the error message.

Could you please give me a suggestion?

 

Atsutoshi Okabe

 

 



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Received on Thu Jan 12 2006 - 06:10:05 PST
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