Thank you very much Anthony,I will try it! Ozge
----- Original Message ----- From: "Anthony Cruz Balberdi" <[EMAIL PROTECTED]> To: <[EMAIL PROTECTED]> Cc: <[email protected]> Sent: Monday, March 19, 2007 3:19 PM Subject: Re: [gmx-users] Appropriate tool to get the number of solventmolecules within a cutoff distance around protein molecule Hi Ozge: You can use a script in VMD to do the work. In VMD you could make various atom selection and use it in the script. You could use something like this: set outfile [open sol_within_prot.dat w]; set nf [molinfo top get numframes] set frame0 [atomselect top "protein" frame 0] # water calculation loop for {set i 1 } {$i < $nf } { incr i } { set prot [atomselect top "protein" frame $i] $prot move [measure fit $prot $frame0] set sol2keep [atomselect top "(same residue as (within 2 of protein)) and resname SOL" frame $i] set nummolP [$sol2keep num] set nummolR [expr $nummolP/3] puts $outfile "$frame $nummolR" puts "$frame" } close $outfile Probably you will need to fit your trajectory if your protein go near the edge of the box because VMD does not take in account the PBC in this type of calculation. Anthony OZGE ENGIN <[EMAIL PROTECTED]> wrote: Hi, I want to calculate the number of solvent molecules within a cutoff distance around the protein molecule. I could not find the appropriate command for this in manual. Moreover, I could not understand the information for g_sorient.Could you give me a more detailed explanation for this? Thanks in advance Ozge Engin _______________________________________________ gmx-users mailing list [email protected] http://www.gromacs.org/mailman/listinfo/gmx-users 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 ------------------------------------------------------------- Antes ahora y siempre COLEGIO University of Puerto Rico at Mayaguez http://www.uprm.edu ------------------------------------------------------------- _______________________________________________ gmx-users mailing list [email protected] http://www.gromacs.org/mailman/listinfo/gmx-users 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 _______________________________________________ gmx-users mailing list [email protected] http://www.gromacs.org/mailman/listinfo/gmx-users 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
