Sorry about that. The university webmail I am using keeps changing the options frequently. I have now tried to send it again as plain text. Hope it comes out ok. The problem I am encountering is this:
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:
>
> This is still unreadable... is there no option for "plain text" or
> "ascii" or something for your email program/account?
>
> On Fri, Jan 22, 2010 at 12:40 PM, Jayalakshmi Sridhar <jsridhar.xula.edu> wrote:
> >
> > <div style="font-family: 'Times New Roman'; font-size: 1 6px;"><br />I was able to solve this problem. But am encount ering a new problem. When reading the reference coordinates it says- < br _moz_dirty="" />rfree: End of file on unit 5.<br _ moz_dirty="" />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.<br _moz_dirty="" />Jaya.<br /> <span>On 01/22/10, <b class="name">Jason Swails </b> <jason.swails.gmail.com>wrote:</span><bloc kquotecite="mid:64de6d71001220858t3181c11fx523bf8dd974d23f.mail .gmail.com" class="iwcQuote" style="border-left: 1px s olid rgb(0, 0, 255); padding-left: 13px; margin-left: 0pt; " type="cite"><div class="mimepart text plain">Could you please copy your email over to plain text? With all of the<br / >markup it is impossible to read your email.<br /><br />Than ks!<br />Jason<br /><br />On Fri, Jan 22, 2010 at 11:5 5
> > AM, Jayalakshmi Sridhar <jsridhar.xula.edu> wrote: <br />><br />> <div style="f ont-family: 'Times New Roman'; font-size: 1 6px;" >Dear Amber Users,<br _moz_dirty="" ; />I have a<br />> protein which I initially heated to 300K and equilibrated for 4 ns. Now I wish to heat t he
> > system further to 325 K. I am using the final 4ns<br />> ;
> > equilibrated system as starting point. I am getting the fol lowing
> > error:<br _moz_dirty="" / ><br _moz_dirty="" /> <br _moz_dirty="" />>$AMB ERHOME/exe/sander -O -i<br />> 2a6_md16.in -p 2a6.p rmtop -c 2a6_md15.rst -r 2a6_md16. rst -o<br />> 2a6_md16.out -x 2a6_md16.mdcrd -ref 2a6_md15.rst <br _moz_dirty="" />>At line 189 of file _rgroup.f< br<br />> _moz_ dirty="" /> Fortran runtime error: End of f ile<br<br />> _moz_dirty="" />< br _moz_dirty="" />The input is<br />> given below:<br _moz_ di rty=""/>&cntrl<br<br/>& gt; _moz_dirty="" /> i min = 0,<br<br />> _m oz_dirty="" /> irest = 1, <br<br />> _moz_dirty= "" /> ntx = 7,<br _ moz_ dirty="" /> ntb = 1, <br _moz_dirty="" /> cut = 10,<br _moz_dirty="" /> ntr = 1,<br _moz_dirty="&q uot; /> 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<br /> > = 0.002<br _moz_dirty="" /> ntpr = 200, ntw x =<br />> 200, ntwr = 2000<br _moz_dirty="" /> /<br _ moz_dirty="" />< ;br _moz_dirty="" />Thank you for t he
> > help.<br _moz_dirty="" />Jaya .<br _moz_dirt y="" /> < ;br /></div><br />><br />> ________________________ _______________________<br
> > />> AMBER mailing list<br />> AMBER.ambermd.o rg<br />> <a href="http://lists.ambermd.org/mailm (http://lists.ambermd.org/mailm) an/listinfo/amber"target="_blank">http://lists.ambermd. (http://lists.ambermd.) org/mailman/listinfo/amber</a><br/>><br/>>< br /><br /><br /><br />-- <br />---------------------- -----------------<br />Jason M. Swails<br />Quantum Theory Pro ject,<br />University of Florida<br />Ph.D. Graduate Stude nt<br />352-392-4032<br /><br />__________ ________________________ _____________<br />AMBER mailing list<br />AMBER.ambermd.org<br /><a href="http://lists.ambe (http://lists.ambe) rmd.org/mailman/listinfo/amber"target="_blank">http://l ists.ambermd.org/mailman/listinfo/amber</a><br/></div>< /blockquote></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 - 10:00:05 PST
