[gmx-users] Removal of Waters in Hydrophobic Core

Justin Lemkul jalemkul at vt.edu
Tue Nov 29 03:12:04 CET 2016 


On 11/28/16 7:02 PM, Christopher Neale wrote:
> You might get more help if you post your script, .gro file, images, etc. somewhere online and link them in a mailing list message. At this point it's impossible to know what is going wrong for your usage with the information you have posted.
>
> I don't know about Justin's scripts. Perhaps they could work together, but you have not said what you want to do.
>
> An alternative is simply to use good selections with "gmx select" to get rid of the waters inside your bilayer.
>

My script might be useful in this case, but only with groups derived from what 
it provides.  It prints index groups of the top and bottom leaflet lipids.  gmx 
traj -ox -com can then be used on a suitable group's P atoms (or some other 
atoms within, e.g. the glycerol moiety) to determine the upper and lower 
coordinate values defining the boundaries of the membrane for removal of water.

But gmx select would also be a good option. Probably faster, too.

-Justin

> ________________________________________
> 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: 28 November 2016 14:26:07
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] Removal of Waters in Hydrophobic Core
>
> 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.
>>
> --
> 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.
>

-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==================================================

More information about the gromacs.org_gmx-users mailing list