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

bharat gupta bharat.85.monu at gmail.com
Mon Jan 31 12:58:57 CET 2011 

I think I answered almost whatever u  asked .. I simulated the structure in
which the chromophore is not there but its constituent residues are there
 i.e. ser 65, tyr 66 and gly 67 .. it means that there is no void in the
structure ..

As I told u in my last mail also that I checked the structure after nvt
equilibration some water molecules were there in the structure ....

I am really sorry for not answering some of ur questions but to my knowledge
whatever u asked I have replied for that ...

On Mon, Jan 31, 2011 at 1:29 AM, bharat gupta <bharat.85.monu at gmail.com>wrote:

>
> I think I answered almost whatever u  asked .. I simulated the structure in
> which the chromophore is not there but its constituent residues are there
>  i.e. ser 65, tyr 66 and gly 67 .. it means that there is no void in the
> structure ..
>
> As I told u in my last mail also that I checked the structure after nvt
> equilibration some water molecules were there in the structure ....
>
> I am really sorry for not answering some of ur questions but to my
> knowledge whatever u asked I have replied for that ...
>
> On Mon, Jan 31, 2011 at 1:13 AM, Mark Abraham <mark.abraham at anu.edu.au>wrote:
>
>>
>>
>> On 01/31/11, *bharat gupta * <bharat.85.monu at gmail.com> wrote:
>>
>> 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 ..
>>
>>
>> Who knows? You've not bothered to answer my question about your
>> chromophore, so I might as well assume it is missing and that genbox is
>> placing waters in the hole.
>>
>>
>> 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 ??
>>
>>
>> genbox describes the criterion it uses. Either it applies to a void in
>> your crystal structure so that waters appear there, or it doesn't. What else
>> can be said?
>>
>>
>>
>> I checked the literature about the crystal structure of GFP and I found
>> that there were water molecules present in the crystal during chromophore
>> formation state .. So it means that water molecules can enter the barrel ??
>> .. will this justification be right ??
>>
>>
>> There are often water molecules in crystal structures. Whether that has
>> bearing on your observations here only you can decide. Get out VMD and look
>> at those waters. While you're at it, look at your starting configuration,
>> like I suggested about 20 emails back. If there's waters in there, then they
>> didn't enter mid-simulation.
>>
>> Anyway, I'm going to desist from trying to help, since you're being too
>> selective about the questions you answer for me to want to use more of my
>> time.
>>
>>
>> Mark
>>
>>
>> On Sun, Jan 30, 2011 at 11:55 PM, bharat gupta <bharat.85.monu at gmail.com>wrote:
>>
>>> 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!
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>>>>> 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
>>>
>>>
>>
>>
>> --
>> 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
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