On 7/24/13 11:30 AM, Shima Arasteh wrote:
Hi,
I am trying to run US on a system composed of lipid bilayer/ ion/ water/
peptide. The peptide is inserted through the lipid bilayer and I' d like to
study the ion conduction through the peptide across the membrane.
In order to do so, I tried to set a specific ion ( Ces with the atom number
85563) as the pull_group1 in mdp file:
pull_group1 = Ces_ion
So I had to get a new group named Ces_ion contains of Ces 85563. Therefore made
a new index file ( index_US.ndx). In this ndx file, there is an extra group in
addition of existed groups as this( The last 2 lines in ndx file) :
[ system]
...
[protein]
...
[protein-H]
...
[ Ces_ion ]
85563
But after running the grompp, I get this fatal error:
File input/output error:
index_US.ndx
Would you please let me know how I would be able to define a new group for a
specific ion ?
Did I make a mistake in defining a new group?
What you did in terms of index group content is fine. The error message means
that the file called "index_US.ndx" is not present in the working directory, or
it has the wrong permissions.
-Justin
--
==================================================
Justin A. Lemkul, Ph.D.
Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalem...@outerbanks.umaryland.edu | (410) 706-7441
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