RE: [gmx-users] Intrinsically disordered proteins
Hi, 1. Thanks for the webpage you provided, I noticed there is a avogadro there, and right now coincidently I have a question relevant to the avogadro, When I tried the avogadro-packmol-extensions, I had installed the avogadro and packmol well, but I do not know where the avogadro plugins/modules can be put ? I tried the put the packmolextension.so under usr/lib/avogadro/1_0/extensions/ but seems not work, Might someone has tried and knew the answer, actually I had asked on the other place, but none feedback. 2. Wow, it's going to be lots of works. lina From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Justin A. Lemkul [jalem...@vt.edu] Sent: Monday, October 18, 2010 9:37 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] Intrinsically disordered proteins #ZHAO LINA# wrote: > Hi, > > 1. For those intrinsically disordered proteins, the sequence is known, > how the simulations will be set up, I mean, the first PDB will be > needed, how to get this one? (Ideally, not necessarily to be practical) > http://www.gromacs.org/Documentation/File_Formats/Coordinate_File#Sources > 2. suppose I got a PDB, there were several models there, let's say 16, > is it acceptable to just take one, say model 1? > Making an arbitrary choice is not a good idea. You have to justify that the model you selected is in some way representative of the ensemble. You could do that by demonstrating that your simulation overlapped the configuration space of the ensemble in the PDB file, i.e. sampled all the expected configurations, thus the starting structure was not an inappropriate bias. -Justin > Thanks for any answering, > > lina > -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee 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 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] Intrinsically disordered proteins
#ZHAO LINA# wrote: Hi, 1. For those intrinsically disordered proteins, the sequence is known, how the simulations will be set up, I mean, the first PDB will be needed, how to get this one? (Ideally, not necessarily to be practical) http://www.gromacs.org/Documentation/File_Formats/Coordinate_File#Sources 2. suppose I got a PDB, there were several models there, let's say 16, is it acceptable to just take one, say model 1? Making an arbitrary choice is not a good idea. You have to justify that the model you selected is in some way representative of the ensemble. You could do that by demonstrating that your simulation overlapped the configuration space of the ensemble in the PDB file, i.e. sampled all the expected configurations, thus the starting structure was not an inappropriate bias. -Justin Thanks for any answering, lina -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee 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
Re: [gmx-users] Intrinsically disordered proteins
On 18/10/10 14:26, #ZHAO LINA# wrote: Hi, 1. For those intrinsically disordered proteins, the sequence is known, how the simulations will be set up, I mean, the first PDB will be needed, how to get this one? (Ideally, not necessarily to be practical) 2. suppose I got a PDB, there were several models there, let's say 16, is it acceptable to just take one, say model 1? Thanks for any answering, That's a theoretical question which has no real "true" answer, given that there is no "true" structure for an IDP, but only an ensemble of structures. I've seen different approaches, from using ROSETTA predictions to simply using random coil structures, to carefully picking ensembles from previous experimentally-restrained simulations. Pick up your favourite approach in the literature, also taking into account what you want to do. m. -- Massimo Sandal, Ph.D. http://devicerandom.org -- 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] Intrinsically disordered proteins
Hi, 1. For those intrinsically disordered proteins, the sequence is known, how the simulations will be set up, I mean, the first PDB will be needed, how to get this one? (Ideally, not necessarily to be practical) 2. suppose I got a PDB, there were several models there, let's say 16, is it acceptable to just take one, say model 1? Thanks for any answering, lina -- 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
