DNA simulation by NAMD

From: sudipta sinha (sudipta.mml_at_gmail.com)
Date: Sun Jul 13 2008 - 06:07:20 CDT

Hi All,

         I have a simple question regarding the simulation of DNA-water
system by NAMD. My problem is generation of .psf file of DNA. I am giving
the DNA.in file which I have used. Here I have considered the two strand of
DNA as a single molecule. By this approach I get a pdb file, where the
two strands are linked by each other in one side and the other side is
open(By VMD, I have seen that). Is this linking serious to simulation? If I
consider the two strand of DNA are two individual segments then the VMD
doesn't show the such type of link. But here my confusion is, if I consider
two strands of DNA are two individual segments (i,e two strands are treated
as two individual molecules) then is it right? I am also curious to know,
where I put the 5TER and 3TER information in DNA.in file? I am eager for
your early reply.

Thanks
Sudipta
*
DNA.in*
topology top_all27_na.rtf
alias residue G GUA
alias atom G O5* O5'
alias atom G C5* C5'
alias atom G 1H5* H5'
alias atom G 2H5* H5''
alias atom G C4* C4'
alias atom G H4* H4'
alias atom G O4* O4'
alias atom G C1* C1'
alias atom G H1* H1'
alias atom G C3* C3'
alias atom G H3* H3'
alias atom G O3* O3'
alias atom G C2* C2'
alias atom G 1H2* H2'
alias atom G 2H2* H2''
alias residue T THY
alias atom T O5* O5'
alias atom T C5* C5'
alias atom T 1H5* H5'
alias atom T 2H5* H5''
alias atom T C4* C4'
alias atom T H4* H4'
alias atom T O4* O4'
alias atom T C1* C1'
alias atom T H1* H1'
alias atom T C3* C3'
alias atom T H3* H3'
alias atom T O3* O3'
alias atom T C2* C2'
alias atom T 1H2* H2'
alias atom T 2H2* H2''
alias atom T 1H5M H51
alias atom T 2H5M H52
alias atom T 3H5M H53
alias residue A ADE
alias atom A O5* O5'
alias atom A C5* C5'
alias atom A 1H5* H5'
alias atom A 2H5* H5''
alias atom A C4* C4'
alias atom A H4* H4'
alias atom A O4* O4'
alias atom A C1* C1'
alias atom A H1* H1'
alias atom A C3* C3'
alias atom A H3* H3'
alias atom A O3* O3'
alias atom A C2* C2'
alias atom A 1H2* H2'
alias atom A 2H2* H2''
alias atom A H62 H62!
alias residue C CYT
alias atom C O5* O5'
alias atom C C5* C5'
alias atom C 1H5* H5'
alias atom C 2H5* H5''
alias atom C C4* C4'
alias atom C H4* H4'
alias atom C O4* O4'
alias atom C C1* C1'
alias atom C H1* H1'
alias atom C C3* C3'
alias atom C H3* H3'
alias atom C O3* O3'
alias atom C C2* C2'
alias atom C 1H2* H2'
alias atom C 2H2* H2''
segment DNA {
         pdb DNA.pdb
}
coordpdb DNA.pdb DNA
segment HOH {
          pdb water_b.pdb
}
coordpdb water_b.pdb HOH
segment SOD {
          pdb NA_ION.pdb
}
coordpdb NA_ION.pdb SOD
guesscoord
writepdb pro_dna_sod_wat.pdb
writepsf pro_dna_sod_wat.psf

This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:49:39 CST