[gmx-users] Removal of Waters in Hydrophobic Core
Sanim Rahman
sanimr at mail.usf.edu
Mon Nov 28 20:26:12 CET 2016
Hey Chris,
Your instruction makes much more sense. I was really confused on what was
the point of generating the keep_these_waters.gro file initially. Thank
you. I have noticed that water molecules were removed from my structure,
however, it removed waters I was not looking for. It took off a random
column of water molecules in my bilayer. What type of data file (gro, top,
pdb, etc.) or graphical interface program is recommended to decide my
upperz and lowerz value?
I know that I am now jumping around with my questions, but are you familiar
with the scripts on the site below? I believe that the bilayer_separator.pl
script could complement the keepbyz.pl script perfectly.
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/scripts.html
Let me know if you would like me to send my current script and the image of
the current model.
Regards,
*Sanim Rahman*
B.S. Chemical Engineering, 2019
Undergraduate Researcher, Global Center for Hearing and Speech Research
On Sat, Nov 26, 2016 at 3:36 PM, Christopher Neale <
chris.neale at alum.utoronto.ca> wrote:
> I have not run that in a long time, but looking at it (and my initial post
> here: https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-
> users/2006-May/021526.html ) it seems like I wrote out the instructions
> incorrectly. Sorry about that!
>
> In the post linked above, step 8 is:
>
> cat not_last_line.gro new_waters.gro last_line.gro > new_system.gro
>
> but I think you would really want to do this:
>
> cat not_last_line.gro keep_these_waters.gro last_line.gro > new_system.gro
>
> where the change is to *actually use* the keep_these_waters.gro file that
> we create with the script ;)
>
> Looks like I realized that a number of years ago:
> http://www.mail-archive.com/gmx-users@gromacs.org/msg37736.html
>
> Sorry for the confusion, indeed the commands listed on the webpage seem
> like they should lead you to recover exactly the initial file :(
>
> Note also that you need to set the upper and lower bounds correctly, and
> modify the script as noted if you are using a 4-point (or 5-ponit) water
> model, and make the noted change if your input file has also velocities.
> All of those things are correctly indicated on the webpage though.
>
> Please reply back to this list if that change works for you as expected
> and I'll bring it to Mark's attention to see if he can update the webpage.
> ________________________________________
> From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <
> gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Sanim
> Rahman <sanimr at mail.usf.edu>
> Sent: 26 November 2016 02:18:09
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] Removal of Waters in Hydrophobic Core
>
> Thank you Chris,
>
> I tried the commands and I was able to obtain an output
> keep_these_waters.gro with about 3.5 MB of data. However, when I continued
> with the rest of the commands:
>
> tail -1 initial.gro > last_line.gro
> head -$(expr $(cat initial.gro | wc -l | awk '{print $1}') - 1 )
> initial.gro > not_last_line.gro
> cat not_last_line.gro new_waters.gro last_line.gro > new_system.gro
> editconf -f new_system.gro -o new_system_sequential_numbers.gro
>
> I still failed to obtain a new structure. The structure is the same as
> solvated.gro. I am going to put extreme z-coordinates to see if all the
> water molecules will be removed. Other than that, do you have any
> suggestions?
>
> *Sanim Rahman*
> B.S. Chemical Engineering, 2019
> Undergraduate Researcher, Global Center for Hearing and Speech Research
>
>
>
> On Fri, Nov 25, 2016 at 3:48 PM, Christopher Neale <
> chris.neale at alum.utoronto.ca> wrote:
>
> > not sure if it is a typo or perhaps a command structure I am unfamiliar
> > with, but I don't understand your command.
> >
> > Try this:
> >
> > chmod +x keepbyz.pl
> > ./keepbyz.pl new_waters.gro > keep_these_waters.gro
> >
> > see here: http://www.gromacs.org/Documentation/How-tos/
> > Membrane_Simulations?highlight=generates
> > ________________________________________
> > From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <
> > gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Sanim
> > Rahman <sanimr at mail.usf.edu>
> > Sent: 24 November 2016 16:12:11
> > To: gromacs.org_gmx-users at maillist.sys.kth.se
> > Subject: [gmx-users] Removal of Waters in Hydrophobic Core
> >
> > Hello,
> >
> > I am currently working through the second tutorial of the Bevan Labs
> KALP15
> > simulation. I am attempting to use the keepbyz.pl script to remove the
> > waters in the hydrophobic core. I have designated a upperz and
> > lowerz coordinated and followed the entire section highlighted in the
> > instructions, however, my output (new_system_sequential_numbers.gro) has
> > no
> > deleted water molecules. It is the same system as solvated.gro.
> >
> > I believe my error is within the keepbyz.pl file, because when I input
> the
> > command:
> >
> > chmod +x keepbyz.pl new_waters.gro > keep_these_waters.gro
> >
> > the file "keep_these_waters.gro" is an empty file.
> >
> > Here is my script for keepbyz.pl:
> >
> > #!/bin/bash
> > # give new_waters.gro as first command line arguement
> > upperz=5.821
> > lowerz=0.574
> > sol=SOL
> > count=0
> > cat $1 | grep "$sol" | while read line; do
> > for first in $line; do
> > break
> > done
> > if [ "$count" = 3 ]; then
> > count=0
> > fi
> > count=$(expr $count + 1)
> > if [ "$count" != 1 ]; then
> > continue
> > fi
> > l=${#line}
> > m=$(expr $l - 24) // would use -48 if velocities are also in .gro and
> > -24 otherwise
> > i=1
> > for word in ${line:$m}; do
> > if [ "$i" = 1 ]; then
> > popex=$word
> > else
> > if [ "$i" = 2 ]; then
> > popey=$word
> > else
> > if [ "$i" = 3 ]; then
> > popez=$word
> > break
> > fi
> > fi
> > fi
> > i=$(expr $i + 1)
> > done
> > nolx=`echo "$popez > $upperz" | bc`
> > nohx=`echo "$popez < $lowerz" | bc`
> > myno=$(expr $nolx + $nohx)
> > if [ "$myno" != 0 ]; then
> > z=${#first}
> > if [ "$z" != 8 ]; then
> > sfirst="[[:space:]]$first"
> > else
> > sfirst=$first
> > fi
> > `echo grep $sfirst $1`
> > fi
> > done
> >
> > I will appreciate the help!
> >
> > Regards,
> >
> > *Sanim Rahman*
> > B.S. Chemical Engineering, 2019
> > Resident Assistant, Castor Hall Engineering Living Learning Community
> > 2016-2017
> > Undergraduate Researcher, Global Center for Hearing and Speech Research
> > Honors College Engineering Peer Advisor
> > <https://www.linkedin.com/pub/sanim-rahman/108/a64/986>
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at http://www.gromacs.org/
> > Support/Mailing_Lists/GMX-Users_List before posting!
> >
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> > * For (un)subscribe requests visit
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > send a mail to gmx-users-request at gromacs.org.
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at http://www.gromacs.org/
> > Support/Mailing_Lists/GMX-Users_List before posting!
> >
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> > * For (un)subscribe requests visit
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > send a mail to gmx-users-request at gromacs.org.
> >
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/
> Support/Mailing_Lists/GMX-Users_List before posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/
> Support/Mailing_Lists/GMX-Users_List before posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>
More information about the gromacs.org_gmx-users
mailing list