Re: [AMBER] heat further an equilibrated system

From: Jayalakshmi Sridhar <jsridhar.xula.edu>
Date: Fri, 22 Jan 2010 11:57:30 -0600

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
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