Hi,
Thank you Jason for the great idea to build 2'-O methyle RNA. I did as you told
me and it worked, need to change some atom naming in the frcmod of the
modified nucleotides......
Thanks
________________________________
From: Jason Swails <jason.swails.gmail.com>
To: AMBER Mailing List <amber.ambermd.org>
Sent: Thu, 19 August, 2010 16:04:14
Subject: Re: [AMBER] O2'methyl RNA
On Thu, Aug 19, 2010 at 10:34 AM, waleed zalloum
<waleed_zalloum.yahoo.com>wrote:
> 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?
>
Maybe not easily (I don't know how much source code you'd have to modify, if
any, a nab expert would have to comment). One thing you CAN do, though, is
to have nab build the initial structure, then edit the PDB, taking out the
atoms that are not present in the modified RNA and changing the residue name
to match the modified RNA in your leap library file. Then load this into
leap and let leap fill in the missing atoms. This way, the overall
structure of the DNA will be built (properly) by nab, but the modified parts
of the nucleic acids will be added by leap.
Good luck!
Jason
>
> 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
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
>
> _______________________________________________
> 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 Fri Aug 20 2010 - 07:30:05 PDT
