AMBER Archive (2001)

Subject: problem in xleap

From: Monica (monicdbs_at_rurkiu.ernet.in)
Date: Mon Jul 09 2001 - 01:47:48 CDT

Hello amberites,
I am using AMBER6.0 tutorial"AMBER refinement of a DNA duplex"

In xleap I gave command:
gcg = loadpdb cgref1.pdb

then it loaded .pdb file & gave usual messages then when I used command:
saveamberparm gcg prmtop cgref1.x
It gave following :
Checking Unit. WARNING: The unperturbed charge of the
unit: -1.000000 is not zero.
FATAL: Atom .R<D 0>.A<H5T 1> does not have a type.
FATAL: Atom .R<D 0>.A<O1P 2> does not have a type.
FATAL: Atom .R<D 0>.A<O2P 3> does not have a type.
FATAL: Atom .R<D 0>.A<O5' 4> does not have a type.
FATAL: Atom .R<D 0>.A<O3' 5> does not have a type.
FATAL: Atom .R<D 0>.A<1' 6> does not have a type.
FATAL: Atom .R<D 0>.A<C2' 7> does not have a type.
FATAL: Atom .R<D 0>.A<C3' 8> does not have a type.
FATAL: Atom .R<D 0>.A<C4' 9> does not have a type.
FATAL: Atom .R<D 0>.A<C5' 10> does not have a type.
FATAL: Atom .R<D 0>.A<O4' 11> does not have a type.......and so on upto
41th residue number
failed to generate parameters
Parameter file was not saved.
Please help.
Thank you very much
monica