AMBER Archive (2006)

Subject: AMBER: Ringof dna

From: Flora Mactavish (ppyyfpm_at_gwmail.ccc.nottingham.ac.uk)
Date: Thu Jul 13 2006 - 08:14:22 CDT

I am attempting to use amber to analyse a ring of dna. When I load the pdb onto xLEaP and attempt to create prmtop and inpcrd files using the command

saveamberparm ring_94_ter ring_ter_vac.prmtop ring_ter_vac.inpcrd

I get the following error

Checking Unit.
WARNING: The unperturbed charge of the unit: -186.000000 is not zero.
FATAL: Atom .R<DA5 1>.A<P 31> does not have a type.
FATAL: Atom .R<DA5 1>.A<O1P 32> does not have a type.
FATAL: Atom .R<DA5 1>.A<O2P 33> does not have a type.
FATAL: Atom .R<DA5 1>.A<C5T 34> does not have a type.
FATAL: Atom .R<DA5 1>.A<H5T1 35> does not have a type.
FATAL: Atom .R<DA5 1>.A<H5T2 36> does not have a type.
FATAL: Atom .R<DA3 94>.A<O3T 34> does not have a type.
FATAL: Atom .R<DT5 95>.A<P 31> does not have a type.
FATAL: Atom .R<DT5 95>.A<O1P 32> does not have a type.
FATAL: Atom .R<DT5 95>.A<O2P 33> does not have a type.
FATAL: Atom .R<DT5 95>.A<C5T 34> does not have a type.
FATAL: Atom .R<DT5 95>.A<H5T1 35> does not have a type.
FATAL: Atom .R<DT5 95>.A<H5T2 36> does not have a type.
FATAL: Atom .R<DT3 188>.A<O3T 34> does not have a type.
Failed to generate parameters

Is there a command to tell Amber that it is dealing with a ring, or any way around this problem?

Many thanks,
Flora

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