Hi,
The cgrefl.pdb file consists information for all residues. There should be
library files that hold information for each residue that is included in the
pdb file. You have to load these "____.lib" files using the command "
>loadoff _____.lib " in xleap. Only then can xleap recognise the type of
atom specified in the pdb file.
Harshit Patel (patelh2_at_rpi.edu)
Rensselaer Polytechnic Institute
Troy, NY
-----Original Message-----
From: Monica [mailto:monicdbs_at_rurkiu.ernet.in]
Sent: Monday, July 09, 2001 2:48 AM
To: AMBER
Subject: problem in xleap
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
Received on Wed Jul 11 2001 - 08:13:56 PDT
