AMBER Archive (2005)

Subject: AMBER: tleap load pdb file

From: xiaowen (xwfang_at_iastate.edu)
Date: Fri Feb 04 2005 - 15:18:09 CST

Thank David replying my question.

Based on David's suggestions, here is the new results and some explanations.
Briefly, I can say the problem is "leap cannot load pdb file".

1. double-check that the test.leap test suite works on your IBM computer;

cd $AMBERHOME/test/leap> ./Run.tleap
(cannot pass, some error with the input file or in sander)

************************************************************************

Running leap tests on ./tleap -> ../../exe/teLeap

    building force field libraries:

        '91 ff.. "(all 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)

*****************************************************************************

2. try to make a smaller version of nuc.pdb, to see if that will work.
I modify nuc.in to:
******************************************
NUC 1
D
A5 A A A A3
NUC 2
T5 T T T T3
END
$ABDNA
*******************************************
$AMBERHOME/exe> nucgen -O -i nuc2.in -o nuc2.out -d
$AMBERHOME/dat/leap/parm/nucgen.dat -p nuc2.pdb

so far is fine, the nuc2.pdb can be open by internet Explorer.
But go to
test=loadpdb nuc2.pdb
the same result as nuc.pdb's

3 I try to use the exist unit to do next steps.
under tleap: ( try small unit ACE)
>saveamberparm ACE ACE.prmtop ACE.inpcrd (works well)
           (if under Xleap, Xwin still cannot show the graphy on unit editor
window)
>test1=copy ACE
>test2=copy ACE
>solvatebox test1 TIP3PBOX 8.0 (WORKS WELL)
>solvateoct test2 TIP3PBOX8.0 (WOKRS WELL)

> Is there actually a chainid "T" in the input? How many atoms does it have?

Yes, the nuc.in file: total number of atoms is 438 from the nuc.pdb file.

*************************************************
NUC 1
D
A5 A A A A A A A A A3
NUC 2
D
T5 T T T T T T T T T3
END
$ABDNA

***************************************************

Your suggestions and ideas are really helpful to a new UNIX and amber user.
Best regards!
xiaowen

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