Hi Justin Thank you for the reply. I have got my answer and its clear now. Regards Sreeta On 19 June 2012 16:55, Justin A. Lemkul [via GROMACS] < [email protected]> wrote:
> > > On 6/19/12 4:49 PM, sreeta.g wrote: > > Hi Justin > > Thank you for the reply. However, PRODRG is used to generate topologies > > from simple pdb files. I am clear on how to create the pdb files for > > Well, it can also provide a simple way to generate coordinate files. It's > a bit > less convenient now that you need a license key, but in any case, there > are > plenty of ways to generate coordinate files. PRODRG isn't really > convenient, I > just recall using it in that particular instance. > > > polymers in general (The entire long chain, with as many molecules as > > required, using MS modelling.) My question, however is about how to > arrive > > at the pdb file. The pdb file that is described in the earlier procedure > > has groups EthB, Eth, EthE and I am surprised because these groups are > > neighboring groups in the pdb file mentioned, which is not intuitive. I > am > > It's not a very good polymer, per se, it's just an example. It is a > boiled > down, instructional demonstration with a system that is as simple as > possible > while still maintaining all necessary features (starting, middle, and > ending > residues). > > > interested in knowing how to create the pdb file using the beginning > middle > > and ending groups as described in the tutorial (rather than the entire > > length of chain). > > The names were modified using a simple text editor. You can have any > arbitrary > number of internal monomer units, the only requirement in the proposed > workflow > is that the beginning and ending residues have some unique names. You can > have > a million internal monomers with the same name (Eth or whatever) as long > as the > ends are different. > > -Justin > > -- > ======================================== > > Justin A. Lemkul, Ph.D. > Research Scientist > 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 [hidden > email]<http://user/SendEmail.jtp?type=node&node=4998714&i=0> > 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 [hidden > email]<http://user/SendEmail.jtp?type=node&node=4998714&i=1>. > > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > ------------------------------ > If you reply to this email, your message will be added to the discussion > below: > > http://gromacs.5086.n6.nabble.com/Regarding-pdb-file-of-a-polymer-tp4998711p4998714.html > To unsubscribe from Regarding pdb file of a polymer, click > here<http://gromacs.5086.n6.nabble.com/template/NamlServlet.jtp?macro=unsubscribe_by_code&node=4998711&code=c3JlZXRhc2FpQGdtYWlsLmNvbXw0OTk4NzExfDg4OTk3NDA=> > . > NAML<http://gromacs.5086.n6.nabble.com/template/NamlServlet.jtp?macro=macro_viewer&id=instant_html%21nabble%3Aemail.naml&base=nabble.naml.namespaces.BasicNamespace-nabble.view.web.template.NabbleNamespace-nabble.view.web.template.NodeNamespace&breadcrumbs=notify_subscribers%21nabble%3Aemail.naml-instant_emails%21nabble%3Aemail.naml-send_instant_email%21nabble%3Aemail.naml> > -- Sreeta Gorripaty -- View this message in context: http://gromacs.5086.n6.nabble.com/Regarding-pdb-file-of-a-polymer-tp4998711p4998715.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing list [email protected] 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 [email protected]. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
