[AMBER] Problems running NAB scripts in the manual

From: Alexander Button <alexander.button.student.adelaide.edu.au>
Date: Wed, 17 Jul 2013 16:38:09 +0930

Dear AMBER users,

I am currently attempting to construct an anti-parallel DNA triplex in
AMBER12 using the program NAB. I have started by looking at the manual and
trying to execute the example scripts in the NAB introduction section
"Structure Quality and Energetics" which are used to produce a parallel DNA
triplex dimer. The scripts which I have attempted to execute are the
script program_5.nab which generates the lowest energy base triad for three
given bases and the script program_6.nab which assembles the triads into
the lowest energy dimer.
I have encountered problems running both these scripts despite the fact
that the scripts and all inputs were copied directly from the examples
directory in the amber12 package .

For the first script I ran the program with input program_5.tat.in however
I kept getting an error message saying that it could not find the residue
THY within the all_nucleic94.lib library file. I looked in the library and
noticed that there were no residues called ADE THY CYT or GUA rather these
bases were called DA DT DC and DG. Assuming that this was the problem I
changed the line

tr = getres( tb, "all_nucleic94.lib" );


tr = getresidue( tb, "all_nucleic94.lib" );

and changed tb in the input file to DT

The script seemed to work from there moving onto the next section of the
code in which the builtin function get_prm is used to get the parameters of
the temp.pdb file using the force field leparc.ff994 however I got another
error message saying that it could not find the file leaprc,ff94. I looked
in the cmd directory and found that leaprc.ff94 was actually in a
subdirectory called oldff. I then copied the pwd output in this directory
and pasted that into the script as giving the following line

m = getpdb_prm( "temp.pdb", "/opt/amber12/dat/leap/cmd/oldff/leaprc.ff94",
"", 0 );

this then seemed to read the leaprc.ff94 file however I got another error
message saying

Reading parm file (tprmtop)
Error: EOF when searching for tprmtop

I then decided to change the force field to the leaprc.99SB force field.
The script then successfully ran giving me the outputs taDT.triad.min.pdb
and taDT.energy.dat. I examined the pdb and found that it contained two
residues in a Watson-Crick base pair arrangement and one residue (the third
base ) perpendicular to the other two and on top of some of the atoms. This
was the same as the initial temp.pdb. I then examined the taDT.energy.dat
file and found that energy for the molecule for the various orientation of
the third base all had exactly the same energy which was 33828178.294.

Because this script wasn't working I decided to move onto the second script
program_6.nab. I generated the triads myself in xleap using the
leaprc.ff99SB force fields and edited the pdb files so that they could be
run in program_6.nab (added in strand names and moved the x,y,z columns
into appropriate positions) the input file was called tat_min.pdb. I ran
for two tat triads and found that it gave me a reasonably good looking
triplex dimer. I then edited the script with a for-loop so that I could
make larger triplexes and renamed the script construct_triplex.nab. I then
re-ran this for a larger number of tat triads and found I got good looking
triplex structures.
After this I tried running the script for triplexes composed of tat and cgc
triads and found that I got residues overlapped on top of each other and
that the P and O3' were not lined up properly to form a bond. To fix this I
tried minimizing the structure using SANDER however after one iteration I
got infinite energy.

I tried using this code for the tat.traid.min.pdb and cgc.triad.min.pdb
triads given in the examples folder however the same problem occurred. I'm
not really sure whats going on but any help on the matter would be greatly

Sincerely yours Alex Button

NOTE:I've attached all the files I've mentioned in this email

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Received on Wed Jul 17 2013 - 00:30:02 PDT
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