Hello, Dear ambers,
I installed AMBER8 on unix and installed X-win32 on windows computer. By using
x-windows terminal, I follow everything from the tutorial 1 to 3 to generate
nuc.pdb, loadpdb and so on.
$AMBERHOME/exe/xleap -s -f $AMBERHOME/dat/leap/cmd/leaprc.ff99
so far, everything is fine, same as the tutorial showed us.
dna1=loadpdb "nuc.pdb"
message as following:
============================================================
dna1=loadpdb "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)
Matching PDB residue name to LEaP variables.
(Residue 0: Terminal/last, was not found in name map.)
Unknown residue: number: 0 type: Terminal/last
..relaxing end constraints to try for a dbase match
-no luck
Created a new atom named: within residue: .R<536870912>
total atoms in file: 438
The file contained 1 atoms not in residue templates.
=============================================================
edit dna1
graphic window come out but did nothing. no graphy.
Is the problem from my installation or from This X-windows, or others, like
unix computer's memory (now it is 1 Gb)?
Then,
I go to the $AMBERHOME/test/make test
stop in
cd qmmm/standard; ./Run.lysine
=================================================
exec():0509-036 cannot load program ../../../exe/sander.QMMM because of the
following errors: 0509-026 system error: there is not enough memory available
now.
../Run.lysine: Program error
make: 1254-004 the error code from the last command is 1.
stop.
==================================================
then,
I go to: $AMBERHOME/test/leap/Run.tleap
*************************************************************
Running leap tests on ./tleap -> ../../exe/teLeap
building force field libraries:
'91 ff..
diffing ../../dat/leap/lib/all_amino91.lib with all_amino91.lib
PASSED
==============================================================
diffing ../../dat/leap/lib/all_aminoct91.lib with all_aminoct91.lib
PASSED
==============================================================
diffing ../../dat/leap/lib/all_aminont91.lib with all_aminont91.lib
PASSED
==============================================================
diffing ../../dat/leap/lib/all_nucleic91.lib with all_nucleic91.lib
PASSED
==============================================================
diffing ../../dat/leap/lib/ions91.lib with ions91.lib
PASSED
==============================================================
'94 ff..
diffing ../../dat/leap/lib/all_amino94.lib with all_amino94.lib
PASSED
==============================================================
diffing ../../dat/leap/lib/all_aminoct94.lib with all_aminoct94.lib
PASSED
==============================================================
diffing ../../dat/leap/lib/all_aminont94.lib with all_aminont94.lib
PASSED
==============================================================
diffing ../../dat/leap/lib/all_nucleic94.lib with all_nucleic94.lib
PASSED
==============================================================
diffing ../../dat/leap/lib/ions94.lib with ions94.lib
PASSED
==============================================================
loadpdb and saveamberparm: 94 ff..
- aminoan94
comparing topology to earlier leap version..
diffing ff94/all_aminoan94.top with all_aminoan94.top
possible FAILURE: check all_aminoan94.top.dif
==============================================================
comparing sander energies
1525-001 The READ statement on the file all_aminoan94.crd cannot be completed
because the end of the file was reached. The program will stop.
Run.tleap: Program error in sander (could be leap input problem)
***************************************************************************
I don't know whether these problems are relative or not.
Any helps and suggestions are appreciated!
Best regards!
xiaowen
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Received on Fri Jan 28 2005 - 05:53:00 PST
