Re: [gmx-users] Fw:some waters in active site of receptor
On 2/16/13 8:37 PM, aixintiankong wrote: Forwarding messages From: aixintiankong Date: 2013-02-16 23:54:51 To: gmx-users@gromacs.org Subject: some waters in active site of receptor Dear, there are three waters in active site of receptor, mediating the binding of ligand with target protein. i want to study the three waters how to affect the binding of ligand with target protein and the contribution to the stability of the system. In order to study the role of the waters, i want to compare some diffrent system models. The first model have all a waters in active site ,the second model have two waters and the third have one water , the fourth have none water in acitve site. however, i don't know how to construct simulation models of those. when i use the genbox program to add solvent to my system, i find there are many other waters being added to the active site and i think the waters which are added by genbox program maybe replace the initial three waters and then i can't study the waters in active site. please hlpe me and then tell me how to do it genbox does not replace water molecules, it only adds more. Your original three waters should always be the first three listed after the end of the protein/ligand coordinates. You could always temporarily rename them (from SOL to HOH, for instance), run the solvation, and verify this yourself. Running genion is the trickier part because the waters of interest stand a small chance of being randomly replaced, though the same renaming strategy could apply. As for the intent of the study, that's harder to say, because if there's enough room for more water to flood in, what makes those waters so special? They could easily be exchanged for others that might diffuse in. I'm afraid I don't have any brilliant insights as far as experimental design goes. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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 listgmx-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
[gmx-users] Fw:some waters in active site of receptor
Forwarding messages From: aixintiankong Date: 2013-02-16 23:54:51 To: gmx-users@gromacs.org Subject: some waters in active site of receptor Dear, there are three waters in active site of receptor, mediating the binding of ligand with target protein. i want to study the three waters how to affect the binding of ligand with target protein and the contribution to the stability of the system. In order to study the role of the waters, i want to compare some diffrent system models. The first model have all a waters in active site ,the second model have two waters and the third have one water , the fourth have none water in acitve site. however, i don't know how to construct simulation models of those. when i use the genbox program to add solvent to my system, i find there are many other waters being added to the active site and i think the waters which are added by genbox program maybe replace the initial three waters and then i can't study the waters in active site. please hlpe me and then tell me how to do it Thank you very much! -- gmx-users mailing listgmx-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
[gmx-users] Gromacs 4.6 crushes in PBS queue system
Hi! I have problem in running gromacs 4.6 in PBS queue... I end up with error: [n370:03036] [[19430,0],0]-[[19430,1],8] mca_oob_tcp_msg_recv: readv failed: Connection reset by peer (104) -- mpirun noticed that process rank 18 with PID 616 on node n344 exited on signal 4 (Illegal instruction). -- [n370:03036] 3 more processes have sent help message help-opal-shmem-mmap.txt / mmap on nfs [n370:03036] Set MCA parameter "orte_base_help_aggregate" to 0 to see all help / error messages 3 total processes killed (some possibly by mpirun during cleanup) I run the same pbs files with older gromacs 4.5.5 (installed with the same openmpi, gcc and fftw) and everything is working.. also when I am running gromacs directly on the access node: mpirun -np 32 /home/users/didymos/gromacs/bin/mdrun_mpi -v -deffnm protein-EM-solvated -c protein-EM-solvated.gro it is running OK. Any ideas? Thank you! Best! tomek -- gmx-users mailing listgmx-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
Re: [gmx-users] calculate the size of protein
Hi if you found optimum size for your protein , you must use VMD ---> Tk console , I done it for commands, please see manual of VMD or mailing list. Best Regards Hamid Mosaddeghi From: Tsjerk Wassenaar To: Discussion list for GROMACS users Sent: Saturday, 16 February 2013, 13:19 Subject: Re: [gmx-users] calculate the size of protein Hi KT, If you set a box in any way, editconf writes the size of the box in the input file, the dimensions of the system and the size of the resulting box. Cheers, Tsjerk On Sat, Feb 16, 2013 at 10:42 AM, Kieu Thu Nguyen wrote: > Hi, > > What is the specific editconf command should i use to calculate the > dimensions of fitting box of the protein ? > > Thanks and regards, > KT > > > On Fri, Feb 8, 2013 at 2:03 PM, Kieu Thu Nguyen wrote: > >> Thank Tsjerk ! I mean that i want to determine the dimensions (x, y, z) of >> the protein >> >> >> On Fri, Feb 8, 2013 at 1:48 PM, Tsjerk Wassenaar wrote: >> >>> Hi KT, >>> >>> What do you mean with size? >>> >>> - circumscribed radius: editconf >>> - radius of gyration: g_gyrate >>> - dimensions of fitting box: editconf >>> - volume: g_sas >>> >>> Cheers, >>> >>> Tsjerk >>> >>> On Fri, Feb 8, 2013 at 5:55 AM, Kieu Thu Nguyen >> >wrote: >>> >>> > Dear all, >>> > >>> > I want to calculate the size of the protein. Which tool should i use for >>> > this purpose ? >>> > >>> > Thanks and regards, >>> > KT >>> > -- >>> > 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 >>> > >>> >>> >>> >>> -- >>> Tsjerk A. Wassenaar, Ph.D. >>> >>> post-doctoral researcher >>> Biocomputing Group >>> Department of Biological Sciences >>> 2500 University Drive NW >>> Calgary, AB T2N 1N4 >>> Canada >>> -- >>> 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 >>> >> >> > -- > 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 -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Biocomputing Group Department of Biological Sciences 2500 University Drive NW Calgary, AB T2N 1N4 Canada -- 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 -- gmx-users mailing listgmx-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
Re: [gmx-users] calculate the size of protein
Hi KT, If you set a box in any way, editconf writes the size of the box in the input file, the dimensions of the system and the size of the resulting box. Cheers, Tsjerk On Sat, Feb 16, 2013 at 10:42 AM, Kieu Thu Nguyen wrote: > Hi, > > What is the specific editconf command should i use to calculate the > dimensions of fitting box of the protein ? > > Thanks and regards, > KT > > > On Fri, Feb 8, 2013 at 2:03 PM, Kieu Thu Nguyen wrote: > >> Thank Tsjerk ! I mean that i want to determine the dimensions (x, y, z) of >> the protein >> >> >> On Fri, Feb 8, 2013 at 1:48 PM, Tsjerk Wassenaar wrote: >> >>> Hi KT, >>> >>> What do you mean with size? >>> >>> - circumscribed radius: editconf >>> - radius of gyration: g_gyrate >>> - dimensions of fitting box: editconf >>> - volume: g_sas >>> >>> Cheers, >>> >>> Tsjerk >>> >>> On Fri, Feb 8, 2013 at 5:55 AM, Kieu Thu Nguyen >> >wrote: >>> >>> > Dear all, >>> > >>> > I want to calculate the size of the protein. Which tool should i use for >>> > this purpose ? >>> > >>> > Thanks and regards, >>> > KT >>> > -- >>> > gmx-users mailing listgmx-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 >>> > >>> >>> >>> >>> -- >>> Tsjerk A. Wassenaar, Ph.D. >>> >>> post-doctoral researcher >>> Biocomputing Group >>> Department of Biological Sciences >>> 2500 University Drive NW >>> Calgary, AB T2N 1N4 >>> Canada >>> -- >>> gmx-users mailing listgmx-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 >>> >> >> > -- > gmx-users mailing listgmx-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 -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Biocomputing Group Department of Biological Sciences 2500 University Drive NW Calgary, AB T2N 1N4 Canada -- gmx-users mailing listgmx-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
Re: [gmx-users] Re: Aspartate at high pH
http://www.gromacs.org/Documentation/How-tos/Constant_pH_Simulation On Wed, Feb 13, 2013 at 2:12 PM, Sathish Kumar wrote: > Hai, >I need to do simulation of protein at pH 12.I am unable to do > that can you please tell me how to do and how to set up pH conditions. >Thank You. > > On Wed, Feb 13, 2013 at 6:08 PM, Valentina > wrote: > > > Thank you Tsjerk! > > > > > > > > -- > > View this message in context: > > > http://gromacs.5086.n6.nabble.com/Aspartate-at-high-pH-tp5005500p5005502.html > > Sent from the GROMACS Users Forum mailing list archive at Nabble.com. > > -- > > gmx-users mailing listgmx-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 > > > > > > -- > regards > M.SathishKumar > -- > gmx-users mailing listgmx-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 > -- gmx-users mailing listgmx-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
Re: [gmx-users] calculate the size of protein
Hi, What is the specific editconf command should i use to calculate the dimensions of fitting box of the protein ? Thanks and regards, KT On Fri, Feb 8, 2013 at 2:03 PM, Kieu Thu Nguyen wrote: > Thank Tsjerk ! I mean that i want to determine the dimensions (x, y, z) of > the protein > > > On Fri, Feb 8, 2013 at 1:48 PM, Tsjerk Wassenaar wrote: > >> Hi KT, >> >> What do you mean with size? >> >> - circumscribed radius: editconf >> - radius of gyration: g_gyrate >> - dimensions of fitting box: editconf >> - volume: g_sas >> >> Cheers, >> >> Tsjerk >> >> On Fri, Feb 8, 2013 at 5:55 AM, Kieu Thu Nguyen > >wrote: >> >> > Dear all, >> > >> > I want to calculate the size of the protein. Which tool should i use for >> > this purpose ? >> > >> > Thanks and regards, >> > KT >> > -- >> > gmx-users mailing listgmx-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 >> > >> >> >> >> -- >> Tsjerk A. Wassenaar, Ph.D. >> >> post-doctoral researcher >> Biocomputing Group >> Department of Biological Sciences >> 2500 University Drive NW >> Calgary, AB T2N 1N4 >> Canada >> -- >> gmx-users mailing listgmx-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 >> > > -- gmx-users mailing listgmx-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
