I was able to solve this problem. But am encountering a new problem. When reading the reference coordinates it says-
rfree: End of file on unit 5.
I have specified irest = 1 and ntx = 5 as I am using a .rst file for reference. Should I change anything else? Thanks for the help.
Jaya.
On 01/22/10, Jason Swails <jason.swails.gmail.com> wrote:
>
> Could you please copy your email over to plain text? With all of the
> markup it is impossible to read your email.
>
> Thanks!
> Jason
>
> On Fri, Jan 22, 2010 at 11:55 AM, Jayalakshmi Sridhar <jsridhar.xula.edu> wrote:
> >
> > <div style="font-family: 'Times New Roman'; font-size: 1 6px;">Dear Amber Users,<br _moz_dirty="" />I have a
> > protein which I initially heated to 300K and equilibrated for 4 ns. Now I wish to heat the system further to 325 K. I am using the final 4ns
> > equilibrated system as starting point. I am getting the following error:<br _moz_dirty="" /><br _moz_dirty="" /><br _moz_dirty="" />>$AMBERHOME/exe/sander -O -i
> > 2a6_md16.in -p 2a6.prmtop -c 2a6_md15.rst -r 2a6_md16. rst -o
> > 2a6_md16.out -x 2a6_md16.mdcrd -ref 2a6_md15.rst<br _moz_dirty="" />>At line 189 of file _rgroup.f< br
> > _moz_dirty="" /> Fortran runtime error: End of file<br
> > _moz_dirty="" />< br _moz_dirty="" />The input is
> > given below:<br _moz_ dirty="" />&cntrl<br
> > _moz_dirty="" /> i min = 0,<br
> > _moz_dirty="" /> irest = 1, <br
> > _moz_dirty="" /> ntx = 7,<br _moz_ dirty="" /> ntb = 1,<br _moz_dirty="" /> cut = 10,<br _moz_dirty="" /> ntr = 1,<br _moz_dirty="" /> ntc = 2,<br _moz_dirty="" /> ntf = 2,<br _ moz_dirty="" /> tempi = 300.0,<br _moz_dirty ="" /> temp0 = 350.0,<br _moz_dirty="" / > ntt = 3,<br _moz_dirty="" /> gamma_ ln = 1.0,<br _moz_dirty="" /> nstlim = 20000, dt
> > = 0.002<br _moz_dirty="" /> ntpr = 200, ntw x =
> > 200, ntwr = 2000<br _moz_dirty="" /> /<br _ moz_dirty="" /><br _moz_dirty="" />Thank you for the help.<br _moz_dirty="" />Jaya.<br _moz_dirt y="" /> <br /></div>
> >
> > _______________________________________________
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> >
> >
>
>
>
> --
> ---------------------------------------
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Graduate Student
> 352-392-4032
>
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Received on Fri Jan 22 2010 - 10:30:03 PST
