Okay, thanks a lot. Majid
________________________________ From: Justin A. Lemkul <jalem...@vt.edu> To: Discussion list for GROMACS users <gmx-users@gromacs.org> Sent: Sat, April 9, 2011 3:05:48 PM Subject: Re: [gmx-users] Naming of DNA residues, and structure of .pdb file majid hasan wrote: > Dear All, > > I am trying to make sure that the names of dna residues in my .pdb file match >with .rtp file in the Amber forcefield. I looked up the residuetypes.dat file >(attached), and it gives the names for DNA residues, which are of the form, >DX, >DX3, DX5, DXN (X=A,C,T,G). So if I have a residue X, then what is the >difference >between DX, DX3, so on i.e when do I name residue X as DX, and when as DX3, >and >so on? > DX = normal residue DX5 = 5' end DX3 = 3' end > Moreover, can anyone explain me the format of pdb file (attached) i.e what do >different columns represent, so I can change the names of residues without >making any error? > http://www.wwpdb.org/documentation/format32/sect9.html -Justin > Thanks, > Majid > -- ======================================== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ======================================== -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
-- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists