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: [email protected] on behalf of Jennifer Williams Sent: Tue 12/15/2009 11:41 PM To: [email protected] Subject: [gmx-users] g_sdf and visualizing using gOpenMol Hi, 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 [MCM] 1 [MCM] 2 [MCM] 3 [SI] 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, Thanks Jenny -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. -- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [email protected]. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
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