[gmx-users] Removal of Waters in Hydrophobic Core
Sanim Rahman
sanimr at mail.usf.edu
Tue Nov 29 08:30:40 CET 2016
Thank you for the responses.
Here is a Dropbox link to all the files and scripts I am using:
https://www.dropbox.com/sh/tk7syifmtwqmtn0/AABWwtX5XNzzBiJB08kQ-xmca?dl=0
As I mentioned before, I am working through the second tutorial of the
Bevan Labs GROMACS Tutorial (KALP15 in DPPC). I am attempting to remove
waters from the hydrophobic core.
I attempted to remove waters from the hydrophobic core by
specifying z-coordinates since the system is oriented along the z-axis. I
experimented with an extreme range in the script and images I uploaded
(lowerz= 5.000 upperz= 50.000).
Thanks for the assistance! I deeply appreciate the time you have spent with
my situation.
Regards,
*Sanim Rahman*
B.S. Chemical Engineering, 2019
Undergraduate Researcher, Global Center for Hearing and Speech Research
<https://www.linkedin.com/pub/sanim-rahman/108/a64/986>
On Mon, Nov 28, 2016 at 9:11 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>
> 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>
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> --
> ==================================================
>
> 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
>
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