[gmx-users] Re: Regarding pdb file of a polymer
sreetasai at gmail.com
Tue Jun 19 23:02:20 CEST 2012
Thank you for the reply. I have got my answer and its clear now.
On 19 June 2012 16:55, Justin A. Lemkul [via GROMACS] <
ml-node+s5086n4998714h65 at n6.nabble.com> 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
> 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
> > 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
> It's not a very good polymer, per se, it's just an example. It is a
> down, instructional demonstration with a system that is as simple as
> while still maintaining all necessary features (starting, middle, and
> > interested in knowing how to create the pdb file using the beginning
> > 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
> number of internal monomer units, the only requirement in the proposed
> is that the beginning and ending residues have some unique names. You can
> a million internal monomers with the same name (Eth or whatever) as long
> as the
> ends are different.
> Justin A. Lemkul, Ph.D.
> Research Scientist
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> gmx-users mailing list [hidden email]<http://user/SendEmail.jtp?type=node&node=4998714&i=0>
> 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
> 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=>
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.
More information about the gromacs.org_gmx-users