[gmx-users] pdb file

[Justin A. Lemkul]

leila karami wrote:
> my pdb file for dna and protein contains 640 and 1130 atoms 
> respectively. if I want creat a new pdb file for studying pr-dna 
> interaction, should be numbering and order of numbers changed? how?
> 

Numbering is the least of your worries, generating a reasonable starting 
structure is much more difficult, if the protein and DNA molecules are in 
separate structure files.  Once the system is assembled, it can be renumbered 
(genconf -renumber); the order is dependent only upon the order specified in the 
[molecules] directive of the topology.

-Justin

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-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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