Hi,
Sorry because it wasn't clear enough. I am building that RNA from scratch and
I used the sequence command in xleap to build a random structure.
If I want to use nab, could I include the modified RNA bases as I do in xleap,
I mean the library and the frcmod?
Thank you so much
--
Waleed Zalloum,
MSc of pharmacy and Pharmaceutical sciences,
Molecular Modeling
School of Pharmacy and Pharmaceutical Sciences,
Faculty of Medical and Human Sciences,
The University of Manchester
Manchester, UK,
Third year PhD student.
E-mail: waleed_zalloum.yahoo.com
Mobile: +44(0)7853719922
________________________________
From: Jason Swails <jason.swails.gmail.com>
To: AMBER Mailing List <amber.ambermd.org>
Sent: Thu, 19 August, 2010 15:23:41
Subject: Re: [AMBER] O2'methyl RNA
Hello,
On Thu, Aug 19, 2010 at 8:37 AM, waleed zalloum <waleed_zalloum.yahoo.com>wrote:
> Dear AMBER users,
>
> I am modelling an O2'-methyle RNA. I loaded the all_modrna08.lib and the
> all_modrna08.frcmod. Upon loading the frcmod file I get something like
> this:
>
> Unknown keyword: O -C -N*-C in parameter file.
> Unknown keyword: O -C -N*-C in parameter file.
> Unknown keyword: O -C -NA-C in parameter file.
> Unknown keyword: O -C -NA-C in parameter file.
> Unknown keyword: O -C -NA-H in parameter file.
> Unknown keyword: O -C -NC-C in parameter file.
> Unknown keyword: O -C -OS-C in parameter file.
> Unknown keyword: O -P -OS-C in parameter file.
> Unknown keyword: O2-P -OS-C in parameter file.
> Unknown keyword: OH-C -CT-C in parameter file.
> Unknown keyword: OH-C -CT-H in parameter file.
> Unknown keyword: OH-CT-C -O in parameter file.
> Unknown keyword: OH-CT-CM-C in parameter file.
> Unknown keyword: OH-CT-CM-H in parameter file.
> Unknown keyword: OH-CT-CT-C in parameter file.
> Unknown keyword: OH-CT-CT-C in parameter file.
> Unknown keyword: OH-CT-CT-H in parameter file.
> Unknown keyword: OH-CT-CT-H in parameter file.
> Unknown keyword: OH-CT-CT-H in parameter file.
>
This sounds like a bad frcmod file. What does your frcmod look like?
>
>
> Moreover, the structure was geometrically not good and extensively folded,
> and the backbone comes through some bases and I have new bonds. I tried to
> heat
> it up, but the problem was not solved. What I have to do to solve this
> problem?
>
I don't think this verbal description helps too much. Are you building this
DNA from scratch or are you starting from a PDB? Did you build the PDB with
nab or nucgen (nab would be the better choice), or are you just letting the
templates in leap build the system? Leap will not do a very good job, so I
encourage you to use nab if that's what you're doing. See the first
tutorial on ambermd.org/tutorials/ on how to do this.
Good luck!
Jason
>
> Thank you
>
>
> Waleed
>
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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Received on Thu Aug 19 2010 - 08:00:05 PDT
