[gmx-users] pdb file

Justin A. Lemkul jalemkul at vt.edu
Wed Oct 21 14:42:28 CEST 2009

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.


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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


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