AMBER Archive (2005)

Subject: AMBER: tleap load pdb file

From: xiaowen (xwfang_at_iastate.edu)
Date: Fri Feb 04 2005 - 09:44:17 CST

Dear ambers,

Amber8 is installed on IBM-AIX unix computer. Following the tutorails, I learn
how to use LEaP.
My questions:
(1)By using Xwin32 on windows, can open universe edit wondow, after "load" one
pdb file, gave some strange message. "edit" it, the unit window didn't show
the graphy of this pdb file. Dr. Ross help me to check the input pdb files,
works fine on his computer.
(2)then, using tleap to load the pdb file. it gave the same message as
xleap's.
(3)saveamberparm test1 polyAT_vac.prmtop polyAT_vac.inpcrd, "vi" them, they
are empty.

Here is the tleap load pdb message:

> test1=loadpdb nuc.pdb

Loading PDB file: ./nuc.pdb
 (starting new molecule for chain T)
-- residue 536870912: duplicate [] atoms (total 438)

 ATOM NAMES IN EACH RESIDUE MUST BE UNIQUE:
    (same-name atoms are reduced to a single atom)

Unknown residue: number: 0 type: Terminal/last
. relaxing end constraints to try for a dbase match
-no luck
Creating new UNIT for residue: sequence: 536870912
Created a new atom named: witchin residue: .R<536870912>
total atoms in file: 438
the file contained 1 atoms not in residue templates

Look forward to hearing from you all!
Thanks!
xiaowen

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