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.abra...@anu.edu.au>wrote: > > > On 01/31/11, *bharat gupta * <bharat.85.m...@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.abra...@anu.edu.au>wrote: > >> >> >> On 01/31/11, *bharat gupta * <bharat.85.m...@gmail.com> wrote: >> >> >> >> ---------- Forwarded message ---------- >> From: bharat gupta <bharat.85.m...@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@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.abra...@anu.edu.au>wrote: >> >>> >>> >>> >>> On 01/31/11, *bharat gupta * <bharat.85.m...@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 : monu46...@yahoo.com >>> >>> >>> -- >>> gmx-users mailing list gmx-users@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-requ...@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 : monu46...@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 : monu46...@yahoo.com >> >> >> -- >> gmx-users mailing list gmx-users@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-requ...@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 : monu46...@yahoo.com > > > -- > gmx-users mailing list gmx-users@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-requ...@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 : monu46...@yahoo.com
-- gmx-users mailing list gmx-users@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-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists