Re: AMBER: REF file problem

From: Gustavo Seabra <>
Date: Mon, 07 May 2007 08:20:10 -0400

deepti nayar wrote:
> hi all
> thank you so much gustavo for your reply .As per your guidance, i
> changed my input script and thus got it working. But now I am
> encountering one more problem. the ref file that i am inputting into
> gives the following error. I searched the amber archive for this and
> found out that initial coordinate file
> doesnt serves as ref file all the time.
> can u please tell me now where to get that ref file from to make my
> script run.I am attaching my input file and output file.
I'm not sure the problem is in your reference file. I believe you got
the wrong syntax for the 'restraintmask'. When you just use
'restraintmask=1-20', Amber cannot determina what you mena. Are those
atoms 1-20? or residues? So, you need to use some extra symbols to
specify that. The right syntax is described in the manual, Ch. 13.5,
under "AMBMASK".

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Received on Wed May 09 2007 - 06:07:14 PDT
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