[gmx-users] Intrinsically disordered proteins

#ZHAO LINA# ZHAO0139 at e.ntu.edu.sg
Mon Oct 18 15:53:37 CEST 2010


1. Thanks for the webpage you provided, I noticed there is a avogadro there, and  right now coincidently I have a question relevant to the avogadro,

When I tried the avogadro-packmol-extensions, I had installed the avogadro and packmol well, 
but I do not know

where the avogadro plugins/modules can be put ?
I tried the put the packmolextension.so under usr/lib/avogadro/1_0/extensions/ 
but seems not work,

Might someone has tried and knew the answer, actually  I had asked on the other place, but none feedback.

2.  Wow, it's going to be lots of works. 

From: gmx-users-bounces at gromacs.org [gmx-users-bounces at gromacs.org] on behalf of Justin A. Lemkul [jalemkul at vt.edu]
Sent: Monday, October 18, 2010 9:37 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] Intrinsically disordered proteins

#ZHAO LINA# wrote:
> Hi,
> 1. For those intrinsically disordered proteins, the sequence is known,
> how the simulations will be set up, I mean, the first PDB will be
> needed, how to get this one? (Ideally, not necessarily to be practical)


> 2. suppose I got a PDB, there were several models there, let's say 16,
> is it acceptable to just take one, say model 1?

Making an arbitrary choice is not a good idea.  You have to justify that the
model you selected is in some way representative of the ensemble.  You could do
that by demonstrating that your simulation overlapped the configuration space of
the ensemble in the PDB file, i.e. sampled all the expected configurations, thus
the starting structure was not an inappropriate bias.


> Thanks for any answering,
> lina


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080

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