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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--
========================================
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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