AMBER Archive (2006)

Subject: AMBER: RE: hi & question

From: Ross Walker (
Date: Thu Mar 09 2006 - 16:14:02 CST

Dear Rosa,
I am copying your email to the Amber mailing list which is the best place
for these types of questions. See for details on
how to subscribe to the mailing list.
The error you are stems from the fact that you are trying to do a
non-periodic implicit solvent calculation:
ntb=0, igb=1
but are creating a prmtop file that has explicit water and periodic
boundaries defined (solvateoct).
You need to decide specifically what type of simulation you wish to run. If
you are going to do an implicit solvent simulation then you don't need to
add the water with solvateoct. However, if you want to do a periodic
boundary explicit solvent simulation then you should edit your input files
and set ntb=1 (and probably ntb=2 at some points to equilibrate the
pressure) and igb=0. See the DNA tutorial at for some
examples of running implicit and explicit solvent simulations.
Also I note that you are using mpirun -np 8 to run your scripts. This is
fine but when an error occurs it can often complicate things. I always
suggest initially testing your system setup with the serial version of
sander. If all works fine then you can use the parallel version to do the
full run.
I hope this helps
All the best

|\oss Walker

| HPC Consultant and Staff Scientist |
| San Diego Supercomputer Center |
| Tel: +1 858 822 0854 | EMail:- |
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From: r. a. []
Sent: Wednesday, March 08, 2006 22:54
Subject: hi & question

Dear Dr. Walker
For your kind attention...I would like to study the effect of temperature on
my structure(a lipase)...I tried to use the amber 8 manual and your
tutorials to prepare my script files but it doesnt work. I have this error:
ifbox=2 in prmtop file but angle are not correct. I referred to the mailing
list and found your reply about that but my problem is already goes on. I
chose 2003 force field and solvateoct b(my pdb file) TIP3PBOX 10.0 iso
my final results in attachment. could you do me a favour and check it for
me. I know that you are very busy but I could not find any help for fixing
this. I attached my script file too. could you please check it out too.
ReallyThank you in anticipation.I will be very glad if I hear from you.
Your Faithfully

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