[gmx-users] Problem in pullx file
Aswathy
ammasachu at gmail.com
Thu Aug 5 13:58:45 CEST 2010
Let me explain.
Consider the channel of a membrane protein, r57 is a residue at the
extracellular loop in this channel. I docked my ligand to the start of the
channel. ie; just below the r57. (Here the I have not started from the
solvent, but at the mouth of the channel , just below r 57..) Then I pulled
the ligand through the channel(parameters as in the first mail). ie; pulled
in such a way that, initially ligand was just below r57, then moved away
from r57.
Plz check some data from the pullx file.
0.0000 7.74891 -0.754818
0.0200 7.74388 -0.754379
0.0400 7.73726 -0.752573
0.0600 7.73032 -0.756692
0.0800 7.72422 -0.747781
0.1000 7.72041 -0.754858
0.1200 7.71691 -0.744501
..............................................
..............................................
..............................................
1099.8601 8.45571 5.46432
1099.8800 8.45551 -5.46076
1099.9000 8.45817 -5.46827
1099.9200 8.46075 5.46829
1099.9401 8.46317 -5.46782
1099.9601 8.46545 5.46577
1099.9801 8.46565 -5.47014
1100.0000 8.46651 5.46001
Thanks,
Aswathy
On Thu, Aug 5, 2010 at 4:28 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:
>
>
> Aswathy wrote:
>
>
>>
>> On Wed, Aug 4, 2010 at 4:31 PM, Justin A. Lemkul <jalemkul at vt.edu<mailto:
>> jalemkul at vt.edu>> wrote:
>>
>>
>>
>> Aswathy wrote:
>>
>> Dear Gromacs users,
>>
>> I am doing SMD of a ligand pathway, and then want ot do the PMF
>> analysis. Initially I pulled the ligand from extra to
>> intracellular side of the protein. The pull code used are given
>> below.
>>
>> pull = umbrella
>> pull_geometry = distance
>> pull_dim = N N Y
>> pull_start = yes
>> pull_nstxout = 10
>> pull_nstfout = 10
>> pull_ngroups = 1
>> pull_group0 = r_57
>> pull_group1 = r_C1
>> pull_rate1 = 0.005
>> pull_k1 = 1000
>>
>> here group0 is one residue at the extracellular region and r_C1
>> is the side chain Carbon atom of the ligand.
>>
>> My question is , the total length of the channel is almost 40
>> Angstrom and as per my knowledge, when we did the pulling the
>> pullx file will give the coordinate of the ligand through the
>> channel.
>>
>>
>> Not quite. Look at the data labels in the .xvg file. The pullx
>> file contains the coordinates (in all of the pull directions) for
>> the reference group, and then the distance between the reference and
>> the pull group along all pull axes.
>>
>> I am still confused. I have measured the distance between the reference
>> group(residue outside) to the other end of the channel. that is around
>> 40Angstrom. if so, 1dz should give around 40 Angstrom? Because once the
>> pulling completed, the distance between group0 and group1 , should be equal
>> to the length of the channel.
>>
>>
> I guess I still don't understand your setup. Are you pulling a ligand
> through a a channel and then beyond the reference group, out into some
> solvent? Or are you just pulling the length of the channel, such that the
> ligand never exits the channel.
>
> If you're pulling through the entire channel and then out into the solvent,
> the sign of dZ is going to change. It might help if you post the first few
> output lines of pullx.xvg (not the headers and stuff, the actual data), as
> well as the last few. That way I can understand exactly what you're dealing
> with.
>
>
> Sorry that i am repeating the same query, i think I am still preconceived
>> about this. Otherwise could you please suggest some good tutorial for the
>> same . I will read that.
>>
>>
> There is a pulling tutorial on the Gromacs website, but nothing that deals
> with what you're doing. Tutorials are designed to generally guide the user
> through a larger procedure, not explain every small piece of analysis.
>
> -Justin
>
>
>>
>>
>> Even though ligand reaches the opposite end of the channel, in
>> pullx file I am getting around 19 Angstrom in total.
>>
>> Again I calculate the g_dist of the ligand and the center of the
>> channel, it shows around 40 Ang in total . Please find the links
>> provided
>>
>>
>> You're measuring two different things. The pullx distance is given
>> relative to your pull_group0, which you said is a residue on one
>> side of the channel. Then you're using g_dist to measure to the
>> center of the channel.
>>
>> Am I misunderstanding anything about the pullx file.
>>
>> Could you please suggest me where thing get wrong?
>>
>>
>> http://docs.google.com/fileview?id=0B1PyTWWGrqt6N2IyNjNhM2UtMzRiZC00MTJmLTg5ODItODJlMzQ5YTM3OGMy&hl=en
>> <
>> http://docs.google.com/fileview?id=0B1PyTWWGrqt6N2IyNjNhM2UtMzRiZC00MTJmLTg5ODItODJlMzQ5YTM3OGMy&hl=en
>> >
>> <
>> http://docs.google.com/fileview?id=0B1PyTWWGrqt6N2IyNjNhM2UtMzRiZC00MTJmLTg5ODItODJlMzQ5YTM3OGMy&hl=en
>> <
>> http://docs.google.com/fileview?id=0B1PyTWWGrqt6N2IyNjNhM2UtMzRiZC00MTJmLTg5ODItODJlMzQ5YTM3OGMy&hl=en
>> >>
>>
>>
>> http://docs.google.com/fileview?id=0B1PyTWWGrqt6ZWRlZGJkOTgtMGEwYi00MzE0LThiZTEtM2JjNmJkMWU5NDYy&hl=en
>> <
>> http://docs.google.com/fileview?id=0B1PyTWWGrqt6ZWRlZGJkOTgtMGEwYi00MzE0LThiZTEtM2JjNmJkMWU5NDYy&hl=en
>> >
>> <
>> http://docs.google.com/fileview?id=0B1PyTWWGrqt6ZWRlZGJkOTgtMGEwYi00MzE0LThiZTEtM2JjNmJkMWU5NDYy&hl=en
>> <
>> http://docs.google.com/fileview?id=0B1PyTWWGrqt6ZWRlZGJkOTgtMGEwYi00MzE0LThiZTEtM2JjNmJkMWU5NDYy&hl=en
>> >>
>>
>>
>> For some reason these documents are inaccessible. It is probably
>> better to use a site like photobucket and post actual images.
>> Google is great, but not everyone has an account and I've also been
>> told that their usage agreement is troubling, in that anything you
>> upload to Google Docs becomes property of Google. Not something
>> I've looked into, but I don't ever post my research data there.
>>
>>
>> -Justin
>>
>>
>> Thank you,
>> -- -Aswathy
>>
>>
>> -- ========================================
>>
>> Justin A. Lemkul
>> Ph.D. Candidate
>> ICTAS Doctoral Scholar
>> MILES-IGERT Trainee
>> Department of Biochemistry
>> Virginia Tech
>> Blacksburg, VA
>> jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
>>
>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>
>> ========================================
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>>
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>>
>>
>>
>> --
>> Aswathy
>>
>
> --
> ========================================
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
> --
> gmx-users mailing list gmx-users at gromacs.org
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> Please search the archive at http://www.gromacs.org/search before posting!
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--
Aswathy
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