AMBER Archive (2005)

Subject: AMBER: question about xwin load pdb file

From: xiaowen (xwfang_at_iastate.edu)
Date: Thu Jan 27 2005 - 23:04:57 CST


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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