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 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 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). Thank you Sreeta
On 19 June 2012 15:46, Justin A. Lemkul [via GROMACS] < [email protected]> wrote: > > > On 6/19/12 3:17 PM, sreeta.g wrote: > > > Hi > > I am working with Polyvinyl Alcohol polymer. I have been following > > http://lists.gromacs.org/pipermail/gmx-users/2009-March/040125.html > > (procedure by Justin) this thread for a lot of guidance. I have obtained > the > > coordinate file for PVA from other sources, however, I am unable to > > understand how the coordinate file was written in this format. All other > > sources of pdb files for polymers contain a fixed number of atoms and > the > > entire chain is written in the coordinate file. > > Please direct me on this as to how the pdb file mentioned in the link > has > > been created. > > > > I created it with a simple molecule drawing program, probably PRODRG but I > honestly don't remember. It's a toy example, meant to be extremely simple > in > order to illustrate the necessary concepts. Creating a topology for > propane is > otherwise very easy ;) > > -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=4998712&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=4998712&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-tp4998711p4998712.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-tp4998711p4998713.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
