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,
--
Jerrano L. Bowleg
PhD Student
Department of Chemistry
Gwaltney Lab- Hand Lab 1126
Mississippi State University
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Received on Thu May 18 2017 - 13:00:03 PDT
