AMBER Archive (2006)

Subject: Re: Re: AMBER: question about the topology file

From: J. Zhang (jzhang_at_biophy.nju.edu.cn)
Date: Sun Nov 12 2006 - 19:42:20 CST


Many thanks!

======= 2006-11-08 07:18:00 艇壓栖佚嶄亟祇=======

>the excluded atom list will containt atoms with higher number
>that are 1-1, 1-2, 1-3 and 1-4 to this atom. yes, that can be quite
>a few atoms, including all atoms in the same ala residue for the N.
>
>
>J. Zhang wrote:
>
>>Dear AMBER users,
>>
>>
>>I have a question about the excluding list in the EXCLUDED_ATOMS_LIST
>>section in the topology file.
>>
>>By reading the egb.f, I knew that the excluding list is to exclude pairs when
>>calculating the LJ and electrostatics terms. Now my question is, whether this
>>list is used by sander in calculations with explicit water and non-LES simulations?
>>
>>I also take a look at the excluding list, and find something strange. For example,
>>for the first N atom in the residue NALA (the first residue in my protein),
>>the corresponding number of excluded atoms is 12, including all the other atoms
>>in the first residue NALA, as well as the first N atom in the second residue.
>>WHY so many atoms are excluded?
>>
>>I can not track the program to find the answer by myself, since the excluded list
>>is stored in ix() array, which stores so many different kinds of information,
>>making the program is difficult to track.
>>
>>Thank you very much for your help!
>>
>>
>>J. Zhang, Dr.
>>
>>---
>>Institute of Biophysics
>>Nanjing University
>>
>>
>>
>>
>>
>>
>>
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= = = = = = = = = = = = = = = = = = = =
                        

        崑

 
                                 
        J. Zhang
        jzhang_at_biophy.nju.edu.cn
          2006-11-13

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