RE: AMBER: Using AMBER for Carbon nanotubes

From: Ross Walker <>
Date: Wed, 18 May 2005 10:12:29 -0700

Dear Zhang,
Are you trying to load the 40 unit cell system as a single residue or as 40
small residues? Leap was never really designed to work with nano-tubes, it
is designed for bio-polymers which typically form a chain with a single
start and end connection on each residue. I suspect your system is different
to this. You may have to set up each unit as a single residue that has a
single head and tail atom (for connecting to the next residue) and then
create a pdb with the number of units you want. Load it into leap and then
add the missing bonds manually.
Without more info, the prep file you used, leaprc.ff23 etc I can't help much
more I'm afraid. Try the following. If your 40 unit system is made up of 40
residues in leap try creating a single "super" residue that has all 40 units
in it and use this. Alternatively if you already have all 40 units in a
single residue try splitting it into smaller residues and then bonding them
together in leap. You could also try taking two copies of your 20 unit
system that worked and joining them together.
I hope this helps
All the best

|\oss Walker

| Department of Molecular Biology TPC15 |
| The Scripps Research Institute |
| Tel:- +1 858 784 8889 | EMail:- |
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From: [] On Behalf Of
Zhang Yingyan
Sent: 18 May 2005 01:22
Subject: AMBER: Using AMBER for Carbon nanotubes

Dear Amber

I am using AMBER 7 to run MD on single-walled carbon nanotubes. And I have
the follwing problems:

I could run MD on (5,5) armchair nanotubs of length 20 unit cells ( totally
400 Carbon atoms) successfully. But when I tried to run longer nanotubes,
for example, (5,5) with 40 unit cells (800 atoms in total) ), It fails.
Amber said "segmentation fault". The commands are shown as follows:

c1:~/CNT $ tleap -f leaprc.ff23
-I: Adding /share/amber7/dat/leap/prep to search path.
-I: Adding /share/amber7/dat/leap/lib to search path.
-I: Adding /share/amber7/dat/leap/parm to search path.
-I: Adding /share/amber7/dat/leap/cmd to search path.
-f: Source leaprc.ff23.

Welcome to LEaP!
(no leaprc in search path)
Sourcing: ./leaprc.ff23
Log file: ./leap.log
Loading parameters: ./parm23.dat
Loading library: /share/amber7/dat/leap/lib/all_nucleic94.lib
Loading library: /share/amber7/dat/leap/lib/all_amino94.lib
Loading library: /share/amber7/dat/leap/lib/all_aminoct94.lib
Loading library: /share/amber7/dat/leap/lib/all_aminont94.lib
Loading library: /share/amber7/dat/leap/lib/ions94.lib
Loading library: /share/amber7/dat/leap/lib/solvents.lib
Loading Prep file: ./case.prep
Segmentation fault

In this case, I couldn't preform " saveamberparm " command to generate
*.prmtop and *.inpcrd files for the longer tubes' MD simulation

Could you tell me how to deal with the problems?

Your help will be greatly apprecited.

Best regards

Zhang Yingyan

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Received on Wed May 18 2005 - 18:53:00 PDT
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