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, +82-51-583-8343Mobile 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, +82-51-583-8343Mobile 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
