[gmx-users] Re: Regarding pdb file of a polymer

[sreeta.g]

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] <
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
> 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
>
> ========================================
>
>
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-- 
Sreeta Gorripaty


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