Fwd: [gmx-users] Monitoring the water movement during simulation

Mon Jan 31 08:55:15 CET 2011

I selected the water molecules but using atom selection in VMD by using the
following command  "water and within 5 of resid 65 to 67", 65 to 67 is the
chromophore position ... some 2 or 3 water molecules were found near to the
chromophore i.e. inside the beta barrel ... Practically it should not happen
..

Also I checked the structure that I saved after genbox command .. and I
found some 3 water molecules inside the barrel .. After reading about genbox
.. what I understood is that it solvates the protein in specified solvent
... but still i donot understand whether during solvation step the water
will go inside the barrel or not ... pls help as its a bit confusing ??

On Sun, Jan 30, 2011 at 11:40 PM, Mark Abraham <mark.abraham at anu.edu.au>wrote:

>
>
> On 01/31/11, *bharat gupta * <bharat.85.monu at gmail.com> wrote:
>
> I followed the lysozyme tutorial step by step and everything seems to be
> fine and the literature cannot be wrong as it has been proved ..
>
>
> Is your model of the chromophore reasonable? IIRC forming the chromophore
> requires making some new bonds.
>
>
> I have repeated this simulation second time...
>
> If you don't tell us how you assessed "2 water molecules have been tracked
> to interact with chromophore" in such a way that somebody could (in
> principle) repeat it, then we'll just assume you've done it wrongly.
>
> "I called g_select with <these inputs> to make an index file, then used
> editconf like <this> with that index file to make a subset structure and
> loaded that in VMD to compare with the original structure, and saw <this>"
> is a method.
>
> Then you asked how to see whether the loops were letting water in. If there
> were waters interacting with the chromophore, then it seems you've proved
> they were letting water in. But that hinges on whether we believe your
> previous statements :-)
>
>
> I want to ask one thing that during solvation step and equilibration step
> water is mixed with the protein so it means that the structure should not
> have water inside it during equilibration step itself or not ?
>
>
> Read genbox -h
>
>
> Mark
>
> On Sun, Jan 30, 2011 at 10:34 PM, Mark Abraham <mark.abraham at anu.edu.au>wrote:
>
>>
>>
>> On 01/31/11, *bharat gupta * <bharat.85.monu at gmail.com> wrote:
>>
>>
>>
>> ---------- Forwarded message ----------
>> From: bharat gupta <bharat.85.monu at gmail.com>
>> Date: Sun, Jan 30, 2011 at 9:30 PM
>> Subject: Re: [gmx-users] Monitoring the water movement during simulation
>> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>>
>>
>> I tracked the movement of water molecules around residues 65 to 67 of my
>> protein (GFP crystal structure) .. According to the literature water should
>> not enter the protein (reason being the cage like structure of GFP) .. but
>> in VMD, 2 water molecules have been tracked to interact with chromophore ...
>> So , I am a bit confused as it should not have happened ??
>>
>>
>> We can't tell. We don't know if your simulation model is flawed, the
>> literature is wrong, your modified GFP do let water in, or your observations
>> of "interacting with the chromophore" aren't right.
>>
>>
>> ... For my analysis  I need to check whether the water is entering the
>> protein or not .. Since I have simulated some variant structures (long
>> loops) of GFP and I need to check how this structure would or would not lead
>> to the entrance of water ??
>>
>>
>> To observe a transit, look for snapshots where they were in one place, and
>> snapshots where they were in another.
>>
>> Mark
>>
>>
>>
>>
>> On Sun, Jan 30, 2011 at 8:20 PM, Mark Abraham <mark.abraham at anu.edu.au>wrote:
>>
>>>
>>>
>>>
>>> On 01/31/11, *bharat gupta * <bharat.85.monu at gmail.com> wrote:
>>>
>>> Hi,
>>>
>>> I am completed a 3 ns simulation of a 230 aa protein .. Now I want to
>>> check whether the water is entering the proteins and through which side of
>>> the protein .. Since the whole protein is surrounded by water I don't know
>>> how this can be done .. is there any command to check .. also I have tried
>>> doing it in VMD but there I am not able to do so ??
>>>
>>>
>>> Use g_select to create index groups of waters within a known distance of
>>> a central point. Then look at those groups in VMD.
>>>
>>> Mark
>>>
>>>
>>>
>>>
>>> Pls help
>>>
>>> --
>>> Bharat
>>> Ph.D. Candidate
>>> Room No. : 7202A, 2nd Floor
>>> Biomolecular Engineering Laboratory
>>> Division of Chemical Engineering and Polymer Science
>>> Pusan National University
>>> Busan -609735
>>> South Korea
>>> Lab phone no. - +82-51-510-3680, +82-51-583-8343
>>> Mobile no. - 010-5818-3680
>>> E-mail : monu46010 at yahoo.com
>>>
>>>
>>> --
>>> gmx-users mailing list    gmx-users at gromacs.org
>>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>>> Please search the archive at
>>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
>>> Please don't post (un)subscribe requests to the list. Use the
>>> www interface or send it to gmx-users-request at gromacs.org.
>>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>>
>>
>>
>>
>>
>> --
>> Bharat
>> Ph.D. Candidate
>> Room No. : 7202A, 2nd Floor
>> Biomolecular Engineering Laboratory
>> Division of Chemical Engineering and Polymer Science
>> Pusan National University
>> Busan -609735
>> South Korea
>> Lab phone no. - +82-51-510-3680, +82-51-583-8343
>> Mobile no. - 010-5818-3680
>> E-mail : monu46010 at yahoo.com
>>
>>
>>
>>
>> --
>> Bharat
>> Ph.D. Candidate
>> Room No. : 7202A, 2nd Floor
>> Biomolecular Engineering Laboratory
>> Division of Chemical Engineering and Polymer Science
>> Pusan National University
>> Busan -609735
>> South Korea
>> Lab phone no. - +82-51-510-3680, +82-51-583-8343
>> Mobile no. - 010-5818-3680
>> E-mail : monu46010 at yahoo.com
>>
>>
>> --
>> gmx-users mailing list    gmx-users at gromacs.org
>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>> Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
>> Please don't post (un)subscribe requests to the list. Use the
>> www interface or send it to gmx-users-request at gromacs.org.
>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>
>
>
> --
> Bharat
> Ph.D. Candidate
> Room No. : 7202A, 2nd Floor
> Biomolecular Engineering Laboratory
> Division of Chemical Engineering and Polymer Science
> Pusan National University
> Busan -609735
> South Korea
> Lab phone no. - +82-51-510-3680, +82-51-583-8343
> Mobile no. - 010-5818-3680
> E-mail : monu46010 at yahoo.com
>
>
> --
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>

-- 
Bharat
Ph.D. Candidate
Room No. : 7202A, 2nd Floor
Biomolecular Engineering Laboratory
Division of Chemical Engineering and Polymer Science
Pusan National University
Busan -609735
South Korea
Lab phone no. - +82-51-510-3680, +82-51-583-8343
Mobile no. - 010-5818-3680
E-mail : monu46010 at yahoo.com
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20110130/c4b24563/attachment.html>