AMBER: some questions about minimization and MD of DNA duplex with sander

From: Chengwen Chen <>
Date: Wed, 31 Jan 2007 15:44:13 +0800

Dear all,

I am simulating DNA decamer bound by drugs.
I adopt the minimiztion & MD simulation method in explicit model of "AMBER
basic tutorial B1-*Simulating a DNA polyA-polyT Decamer*". The starting
structure is NMR solution structure, and the MD simulation time is 3ns.
Cause I want to compare simulated structure with starting structure, the
average structure of last 2ns of simulation (minimization is followed) is
taken as my 'simulated strucuture'. (the water box is stipped when average
the structure with ptraj). The RMSD of "simulated structure" & starting
structure is about 3A.

Now, I have some question about the simulation and analysing method.

1. Minimiztion steps:
Before the MD simulation, 7000 steps (2000 for minimizing water box, 5000
for whole system) of minimization is applied. The RMS value of last step is
1.5584E-01. Is it enough? Should I further minimize the system when RMS is
less than 1.0E-03, or even 1.0E-04?

2. Analysis of md result:
I noticed that average structure of the overall simulation may not be
reasonable for comparison. Can I take the conformation with lowest energy as
"simulated structure"?
Some published papers provided a analysing method: use CARNAL module of
amber to determine average structures for different conformational families.
But I can't find "carnal" at AMBER9, not even the manual mention this. Is
"CARNAL" avaliable in AMBER9? If not, is there any other module can be used

4. minimization of average strucuture:
Even I get the average structures for different conformational families, the
minimization of average strucures is still needed. So the question of
minimization steps still exits. I reviewed the reply of similar questions at
AMBER maillist, most recommend a small number of minimiztion steps. But I am
confused. Why not minimize the system to meet converge critia, like RMS=
1.0E-03, or 1.0E-04?

Sorry for asking so many question at one time. Any comments and reply would
help me a lot. Thank you.

Best Wishes

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Received on Sun Feb 04 2007 - 06:07:03 PST
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