[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.

Catch ya,

Dr Dallas Warren
Pharmacy and Pharmaceutical Sciences
Monash University

A polar bear is a Cartesian bear that has undergone a polar transformation

-----Original Message-----
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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