Re: [gmx-users] Appropriate tool to get the number of solvent molecules 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
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Antes ahora y siempre COLEGIO
University of Puerto Rico at Mayaguez
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Re: Re: [gmx-users] Appropriate tool to get the number of solvent molecules within a cutoff distance around protein molecule
Thank you very much for your attention! Best regards, Ozge Engin -Original Message- From: Yang Ye <[EMAIL PROTECTED]> To: Discussion list for GROMACS users Date: Sun, 18 Mar 2007 00:35:13 +0800 Subject: Re: [gmx-users] Appropriate tool to get the number of solvent molecules within a cutoff distance around protein molecule try g_trjorder. Some code modification may be needed. Regards, Yang Ye OZGE ENGIN 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 listgmx-users@gromacs.org > 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 listgmx-users@gromacs.org 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 listgmx-users@gromacs.org 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
Re: [gmx-users] Appropriate tool to get the number of solvent molecules within a cutoff distance around protein molecule
try g_trjorder. Some code modification may be needed. Regards, Yang Ye OZGE ENGIN 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 listgmx-users@gromacs.org 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 listgmx-users@gromacs.org 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
Re: [gmx-users] Appropriate tool to get the number of solvent molecules within a cutoff distance around protein molecule
Hi. g_hbond can do that, sort of. You can calculate e.g. the nr of water oxygens within a certain distance from the protein. The limitation lies in that g_hbond operates at a atom basis, not molecule, meaning that there is strictly no way of finding the number of solvent molecules directly. However, I think that counting the nr of water oxygens would be good enough for most applications. /Erik 17 mar 2007 kl. 11.17 skrev OZGE ENGIN: 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 listgmx-users@gromacs.org 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 ___ Erik Marklund, PhD student Laboratory of Molecular Biophysics, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: +46 18 471 4537 fax: +46 18 511 755 [EMAIL PROTECTED] http://xray.bmc.uu.se/molbiophys ___ gmx-users mailing listgmx-users@gromacs.org 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] Appropriate tool to get the number of solvent molecules within a cutoff distance around protein molecule
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 listgmx-users@gromacs.org 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] Appropriate tool to get the number of solvent molecules within a cutoff distance around protein molecule
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 listgmx-users@gromacs.org 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
