HI,
The problem is that you have a terminal base (U5/A5), but you also have a
(multiple?) phosphate groups on it- any of the end 5' bases by definition
won't have the phosphate group on it, so you'd need to cut it off in your
input pdb.
Best,
Kenneth
On Fri, Mar 12, 2021 at 6:10 AM richa anand <richaaanand.gmail.com> wrote:
> Dear Users,
>
> I am using the following input parameters for tleap input. Before it I have
> run pdb4amber also.
>
> Tleap input:
>
> source leaprc.protein.ff14SB
> source leaprc.RNA.OL3
> source leaprc.water.tip3p
> designed = loadPdb 6mdz-R.amber.pdb
> check designed
> addions designed Na+ 8
> solvatebox designed TIP3PBOX 10.00 0.75
> charge designed
> saveAmberParm designed 6mdz-R.amber.prm.top 6mdz-R.amber.prm.crd
> savepdb designed 6mdz-R.amber.out.pdb
> quit
>
>
> After running, Tleap I am getting this error message again and again:
>
> FATAL: Atom .R<U5 805>.A<OP3 29> does not have a type.
> FATAL: Atom .R<U5 805>.A<P 30> does not have a type.
> FATAL: Atom .R<U5 805>.A<OP1 31> does not have a type.
> FATAL: Atom .R<U5 805>.A<OP2 32> does not have a type.
> FATAL: Atom .R<A5 825>.A<P 32> does not have a type.
> FATAL: Atom .R<A5 825>.A<OP1 33> does not have a type.
> FATAL: Atom .R<A5 825>.A<OP2 34> does not have a type.
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>
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Received on Fri Mar 12 2021 - 22:30:03 PST
