It might be best if you copy/paste your input and the result, but I
think I can guess that your PDB has atom names that don't agree with the
force field, and that if you look closely at your output you will see
these atoms being added to the existing template.
If so, there are two solutions: atom name mapping, and adjusting the
names in your PDB to match.
One dumb but effective way to see what names are expected is to generate
an arbitrary pdb by using leap's sequence command with the residues of
interest, then savepdb and have a look. Or you can e.g. 'desc DT5' to
see the atom names listed, I believe.
If this doesn't apply, input/output, please.
Bill
On 5/18/17 12:48 PM, Jerrano Bowleg wrote:
> I am attempting to use amber to analyse a cMYC G quadruplex structure. When
> I load the pdb onto xLEaP and attempt to create prmtop and inpcrd files
> using the command
>
> saveamberparm cMYC121_vac.prmtop cMYC_vac.inpcrd
>
> I get the following error
>
> Checking Unit.
> FATAL: Atom .R<DT5 1>.A<P 31> does not have a type.
> FATAL: Atom .R<DT5 1>.A<OP1 32> does not have a type.
> FATAL: Atom .R<DT5 1>.A<OP2 33> does not have a type.
> FATAL: Atom .R<DT5 1>.A<OP3 34> does not have a type.
> FATAL: Atom .R<DT5 1>.A<H11 35> does not have a type.
> FATAL: Atom .R<DT 10>.A<N9 33> does not have a type.
> FATAL: Atom .R<DT 10>.A<N7 34> does not have a type.
> FATAL: Atom .R<DT 10>.A<C8 35> does not have a type.
> FATAL: Atom .R<DT 10>.A<H8 36> does not have a type.
> FATAL: Atom .R<DT 10>.A<H2 37> does not have a type.
> FATAL: Atom .R<DT 10>.A<N6 38> does not have a type.
> FATAL: Atom .R<DT 10>.A<H61 39> does not have a type.
> FATAL: Atom .R<DT 10>.A<H62 40> does not have a type.
> FATAL: Atom .R<DA3 23>.A<'HO3 34> does not have a type.
> Failed to generate parameters
> Parameter file was not saved.
>
> Is there a command to tell Amber that it is dealing with this, or any way
> around this problem?
>
> Many thanks,
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Received on Thu May 18 2017 - 13:30:02 PDT
