[gmx-users] g_sdf and visualizing using gOpenMol
Dallas B. Warren
Dallas.Warren at pharm.monash.edu.au
Tue Dec 15 22:25:11 CET 2009
Rename it to .plt might be a good start, since that is the file extension it is meant to have (as noted in the help information for g_sdf).
Also, there is an issue with the reference structure built was the script, it is not correct. Has been noted by a couple of people. Been meaning to check if there is a bug submitted for it.
Dr Dallas Warren
Pharmacy and Pharmaceutical Sciences
A polar bear is a Cartesian bear that has undergone a polar transformation
From: gmx-users-bounces at gromacs.org on behalf of Jennifer Williams
Sent: Tue 12/15/2009 11:41 PM
To: gmx-users at gromacs.org
Subject: [gmx-users] g_sdf and visualizing using gOpenMol
I have a mesoporous silica with attached organic surface groups (alkyl
chains). I am trying to quantify to what extent these surface groups
interact with the mesoporous silica surface they are attached to (as
opposed to projecting straight into the pore space).
I thought about using the g_sdf tool (on one surface group at a time
initially) but am not completely sure what I am doing is correct so I
am hoping someone can guide me. My index file looks like this
4 5 6 7 8 9 10 11 12 13....
Where groups 1, 2 and 3 are carbons of the alkyl chain. SI atoms are
taken to represent the surface of the mesoporous silica. I run g_sdf
in gromacs and get a refmol.gro file (which looks very different to
my structure) and a gom_plt.dat file. I've installed gOpenMol but I am
having trouble loading the gom_plt.dat file. It is necessary to load
coordinates in first so I load in refmol.gro. As soon as I try to load
the .dat file (using plot> contour>import) the gui window closes and I
get the following
Will apply a physical translation (x,y,z): 12.236523 18.866343 9.419045
Will apply a MT translation (x,y,z): 0.000007 0.000004 0.000002
Minimum value 0.000000 maximum value 134.129913
**** Signal was caught ****
=> : Success
Signal code is: 11, errno
I am not sure whether this is because I have unreasonable data in my
.dat file (or because my refmol.gro file looks strange) or because I
haven't got the hang of using gOpenMol. I don't have any idea what the
contour plot should like. Could someone e-mail me a working
gom_plt.dat file so I can at least check that I can correctly load it
and see what a plot looks like?
Any further advice is appreciated,
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