you need to tell amber WHAT set of coordinate to restraint to!
Add the -ref flag to your pmemd line, and use it as -ref name.crd
On 8/30/16 1:12 PM, Michael Shokhen wrote:
> Dear Bill,
>
>
> Your comment is too short and not clear for me.
>
> Would you please give me more detailed direction
>
> how to correct the script file in order to resolve the problem ?
>
>
> Thank you,
>
> Michael
>
>
>
>
> *****************************
> Michael Shokhen, PhD
> Associate Professor
> Department of Chemistry
> Bar Ilan University,
> Ramat Gan, 52900
> Israel
> email: shokhen.mail.biu.ac.il<https://webmail.biu.ac.il/owa/redir.aspx?C=a160ef9b9a6b4d06992402715d3ee465&URL=mailto%3ashokhen%40mail.biu.ac.il>
> ________________________________
> From: Bill Ross <ross.cgl.ucsf.edu>
> Sent: Tuesday, August 30, 2016 9:59:10 PM
> To: AMBER Mailing List
> Subject: Re: [AMBER] frozen geometry setting?
>
> Note you need to specify your target coords:
>
> Bill
>
>
> On 8/30/16 11:55 AM, Michael Shokhen wrote:
>> | REFC: refc
>
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--
Dr. Adrian E. Roitberg
University of Florida Research Foundation Professor.
Department of Chemistry
University of Florida
roitberg.ufl.edu
352-392-6972
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Received on Tue Aug 30 2016 - 12:30:03 PDT
