Re: [AMBER] RNA xleap

From: Charles Johnson <cjohns98.slu.edu>
Date: Fri, 11 May 2012 13:07:54 -0500

David,

Here is the other message: For atom: .R<Na+ 34>.A<Na+ 1> Could not find type: Na+ I see this same message when I try and save after the addition of TIP4PBOX. I am following the section in the manual on adding ions.

When I specify ff10 it should be adding in ions08.lib and it see that in the printout in the beginning of my xleap session.

Thanks,
Charlie

----
Charles A. Johnson
Ph.D. Candidate
Department of Chemistry
Saint Louis University
Monsanto Hall 214
3501 Laclede Ave.
St. Louis, MO  63103-2010
Fax: (314) 977-2521
Email: cjohns98.slu.edu
On May 11, 2012, at 12:49 PM, David A Case wrote:
> On Fri, May 11, 2012, Charles Johnson wrote:
>> 
>> I am trying to model an RNA duplex using AMBER 11.  When trying to
>> create the water + Na ion .prmtop and .inpcrd files in xleap it keeps
>> giving "Parameter file was not saved" error.  How can I save these
>> files?  I am using leaprc.ff10 when starting xleap.  I am able to create
>> the .prmtop and .inpcrd files for my duplex in vacuum.
> 
> Before printing out the error message listed above, LEaP will also print out a
> error message telling you what the real problem is, such as missing
> parameters, etc.  You need to look at that message.
> 
> [The most common reason is that you did not load a frcmod file for the Na+
> ions; see the section on "Ions" in the "Choosing a force field" chapter.]
> 
> ....dac
> 
> 
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Received on Fri May 11 2012 - 11:30:03 PDT