RE: AMBER: rfree: Error input file

From: Steve Seibold <>
Date: Thu, 24 May 2007 15:22:39 -0400

Hi Carlos

Yes you are correct and I did go back and look at my minimization
inputs. They did indeed have nmropt=1. It was my mistake in thinking
that ntr=1 called for the restraints and the atoms involved.


Thanks, Steve




From: [] On Behalf
Of Carlos Simmerling
Sent: Thursday, May 24, 2007 2:57 PM
Subject: Re: AMBER: rfree: Error input file


unless you set nmropt=1 the weight change and rst sections won't be
sander is trying to read the group input for the positional restraints
you didn't use restraintmask) and it is finding instead the &wt section.

so, two problems:
ntr=1 specifies positional restraints and you have not defined the set
of atoms
using &wt and DISANG needs nmropt=1 to be used.

I'm not sure how this could have worked for minimization, perhaps the
input for that had nmropt=1?

On 5/24/07, Steve Seibold <> wrote:

Hello Amber

I have the following input file that has ntr restraints. The restraint
commands do work when I ran minimization, but fail when I switched to


The input file is:





 ntpr=250, ntwx=2500, ntwr=-2500,


 nstlim=500000, dt=0.002, ntc=1,



 igb=1, intdiel=1, extdiel=2,





 tempi=0, temp0=10,




&wt type='REST', istep1=0, istep2=700, value1=0.1,

    value2=1.0, &end

&wt type='END' &end






The output file showing the error was:



 &wt type='REST', istep1=0, istep2=700, value1=0.1,


     rfree: Error decoding variable 1 3 from:



     this indicates that your input contains


      incorrect information


     field 1 was supposed to


      have a (1=character, 2=integer, 3=decimal) value


I have checked "spacing" by comparing this file with online examples and
nothing stands out to me as to why it should not run. Does anyone else
have an idea as to why this input file is failing?


Thanks, Steve







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Received on Sun May 27 2007 - 06:07:30 PDT
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