On Sun, Nov 14, 2010 at 14:50, leila karami <karami.lei...@gmail.com> wrote: > I made a selection.dat file as follows: > > waterO = group SOL and name OW; > heavy1 = group Protein_A and group "Protein-H"; > heavy2 = group Protein_B and group "Protein-H"; > inter = waterO and within 0.35 of heavy1 and within 0.35 of heavy2; > > is my selection.dat file true?
Your selection.dat only specifies several variables, but never uses any of these; this is the reason why you get the message "Nothing selected". Variable definitions (any lines with an assignment) are only meant as convenient notation and/or for optimization, and do not define selections as such. It appears that what you want to do is accomplished by adding a line "inter;" at the end of the file, or removing "inter =" from the last line. Please take a look at the examples accessible through -select "help examples". > when I used g_select -f .xtc -s .tpr -n .ndx -os -oc -oi -om -on -sf > selection.dat -select, what should be put in front of -select to avoid > Nothing selected, finishing up? You should not use -sf and -select at the same time; at most one of them gets used at a time, as explained in the online help (-select "help cmdline"). It may be that the help is not exactly accurate if you pass an empty string to -select, but nevertheless, these options have not been designed to be used simultaneously. Teemu PS. Please don't send e-mail to me personally. All such questions are better asked on the gmx-users list, where someone else may also be able to help you as well. Also, in this case, the question you sent to the list ~1 hour after the personal e-mail was in fact much more to the point. Without the information contained in the latter, you probably would not have gotten a useful reply. PPS. I'm no longer employed in the academia, so please don't expect an immediate reply. You may cc me on an e-mail to the list if you haven't gotten any reply on the list, and I'll try to take a look when I have sufficient free time. -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
