Hi,
What version of AmberTools are you using? I think the old leaprc.ff99
doesn't have U in there, but the more recent variants (leaprc.ff99SB,
leaprc.ff99bsc0, leaprc.ff10 etc) do.
-Dan
On Wed, Jun 29, 2011 at 2:50 AM, hari krishna <haricoolguy111.gmail.com> wrote:
> Dear Amber team and users:
>
> I am trying to do the MD simulation of RNA and protein complex. While I was
> trying to prepare the AMBER parameter file in the XLeap, I got the following
> error such that it says the unknown residue as Uracil, it is not recognizing
> the Uracil base of RNA and it could identify all other bases such as T A G C
> except U, I am using FF99, is there is any seperate forcefield for RNA, If
> so please suggest me.
>
>
> Error:
>
> Unknown residue: U number: 4 type : non-terminal
> Unknown residue: U number: 7 type : non-terminal
> Unknown residue: U number: 12 type : non-terminal
> Unknown residue: U number: 13 type : non-terminal
>
> ..relaxing end constraints to try for a dbase match
> -no luck
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Received on Wed Jun 29 2011 - 09:00:04 PDT
