AMBER Archive (2004)

Subject: AMBER: Problems with xleap

From: Javier Perez Miron (xavip_at_qorws1.uab.es)
Date: Thu Feb 26 2004 - 19:18:11 CST

Hi everyone!!

I made an optimization in vacuum using SANDER.So, I obtained many files. One of
them is the .rst file. I converted that .rst file into .pdb file using the
ptraj program. After that, I want to load the .pdb file using xleap. I don't
know why but xleap generate other new atoms.

In xleap, I write the next lines:

loadoff unit_name library.lib
unit_name = loadpdb pdb_file.pdb

and the program write the follow lines:

Loading PDB file: ./file.pdb
Unknown residue: HHH number: 0 type: Terminal/last
..relaxing end constraints to try for a dbase match
  -no luck
Unknown residue: HHH number: 1 type: Terminal/last
..relaxing end constraints to try for a dbase match
  -no luck
Unknown residue: HHH number: 2 type: Terminal/beginning
..relaxing end constraints to try for a dbase match
  -no luck
Unknown residue: HHH number: 3 type: Nonterminal
Unknown residue: HHH number: 4 type: Terminal/last
..relaxing end constraints to try for a dbase match
  -no luck
Unknown residue: HHH number: 5 type: Terminal/last
..relaxing end constraints to try for a dbase match
  -no luck
Unknown residue: HHH number: 6 type: Terminal/last
..relaxing end constraints to try for a dbase match
  -no luck
and then,

Creating new UNIT for residue: HHH sequence: 1
...
Creating new UNIT for residue: HHH sequence: 2
...
Creating new UNIT for residue: HHH sequence: 3
...
Creating new UNIT for residue: HHH sequence: 4
...
Creating new UNIT for residue: HHH sequence: 5
...
Creating new UNIT for residue: HHH sequence: 6
...

How can I resolve this problem?

Best regards,

Xavi Perez

Chemoinformatic
Universitat Autonoma de Barcelona
Barcelona, Spain.
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