Re: [AMBER] Simulating a protein with nmr structure

From: Deepangi Pandit <>
Date: Wed, 10 Mar 2010 13:45:12 -0500

Hi Nicholus:
It is clear from Dr. Simmerling's reply that you should simulate more
than one protein structure. I just want to share my thoughts on how to
choose NMR structures from the all models given in the pdb file. Here
are the options

1. You can calculate RMSD of structures after superimposing structures
on backbone atoms of the rigid part(info about the rigid part may be
available from the corresponding published paper). This will give you
a range of values

2. Divide this range in reasonable bins then select a structure from each bin

All the best!

On Wed, Mar 10, 2010 at 6:37 AM, Carlos Simmerling
<> wrote:
> my opinion is that you should simulate more than 1 (for example, choose 2
> and simulate both), and your conclusions should be the same from both
> simulations. if the conclusions depend on which model is chosen, this
> represents uncertainty.
> On Wed, Mar 10, 2010 at 4:50 AM, nicholus bhattacharjee <
>> wrote:
>> Dear community,
>>                          I want to simulate a protein whose structure is
>> elucidated with NMR. As we know there are number of models in the NMR
>> structure PDB file, I am confused which one to chose. Please help.
>> --
>> Nicholus Bhattacharjee
>> PhD Scholar
>> Department of Chemistry
>> University of Delhi
>> Delhi-110007 (INDIA)
>> Phone: 9873098743(M)
>> _______________________________________________
>> AMBER mailing list
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> AMBER mailing list

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Received on Wed Mar 10 2010 - 11:00:04 PST
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