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
>
>
>
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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 Thu Aug 19 2010 - 07:30:06 PDT
