On 6/8/12 5:32 PM, Erica Hicks wrote:
Hi,
I went back and found that a possible error could be that the coordinate file
was not updated correctly. After concatenated the Kalp_newbox.gro and
dppc128_whole.gro, it said to update the coordinate file with the correct
number of atoms. This should be the topology.top, right? But when I look
through this, all I find is:
[ molecules ]
; Compound #mols
Protein 1
Where should the number of atoms be and is topology.top the correct file?
Make sure you added the correct topology information (step 2 in the tutorial,
note the green text):
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/02_topology.html
Step 3.2 tells you:
"Remove unnecessary lines (the box vectors from the KALP structure, the header
information from the DPPC structure) and update the second line of the
coordinate file (total number of atoms) accordingly."
The tutorial assumes you're familiar with such operations, so in reality what
it's implying is that, since you've now concatenated a protein and a 128-lipid
membrane, you need to add:
DPPC 128
to the [molecules] directive (after the Protein line to keep the correct order).
Further manual modifications are necessary based on how many lipids InflateGRO
removes.
-Justin
Erica
________________________________
From: Justin A. Lemkul [via GROMACS] [[email protected]]
Sent: Friday, June 08, 2012 4:02 PM
To: Hicks, Erica
Subject: Re: Energy Minimization - not getting correct lipid area
On 6/8/12 4:57 PM, Erica Hicks wrote:
It was after just one iteration. The number of lipids removed after scaling
the lipids by a factor of 4 was two. I am not sure how to update this as the
[molecules] directive in the topology.top shows only the number of moles,
i.e. 1.
The number shown in [molecules] is the number of molecules of a given species.
If you started with 128 lipids, a removal of 4 means you need to list 124
lipids.
I don't know how you can get such a small area with only one iteration of
shrinking. Your box should be enormous at that point.
-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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========================================
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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