a now I understand that genbox has reorented the order the residues in the protein which was embedded in the membrane used as the solvent >)
is it possible to prevent the order of all residues in the system provided by -cs flag? 2016-04-19 15:14 GMT+02:00 James Starlight <jmsstarli...@gmail.com>: > btw I have tried to insert second molecular using just genbox having > both components oriented properly in the space before > > g_genbox -cp waterSOLprot.gro -cs MEMBRANEsystem.gro -vdwd 0.21 -o > solvatedNEW.gro -box 18 18 28 > > than checking VMD solvatedNEW.gro - everything was looks perfect- the > waterSOLprot has been placed in proper position and overlapped CG > water has been removed. > > now running gromppt I received > > WARNING 1 [file system.top, line 49]: > 2886 non-matching atom names > atom names from system.top will be used > atom names from system.gro will be ignored > > > I also should specify that after genbox I edited new topology.top manually > putting chains of the proteins in correct order (like in new gro file > produced by genbox) and putting correct number of W > > assuming that initially I have multi chain protein in the POPC membrane > and using genbox I added to the system one new chain Z > > before > [quote]Protein_A 1 > Protein_B 1 > Protein_C 1 > Protein_D 1 > Protein_E 1 > Protein_F 1 > Protein_G 1 > Protein_H 1 > Protein_I 1 > Protein_J 1 > Protein_K 1 > Protein_L 1 > Protein_M 1 > POPC 451 > CHOL 0 > POPC 451 > CHOL 0 > W 61226 > NA+ 678 > CL- 671[/quote] > > after > [quote]Protein_Z 1 > Protein_A 1 > Protein_B 1 > Protein_C 1 > Protein_D 1 > Protein_E 1 > Protein_F 1 > Protein_G 1 > Protein_H 1 > Protein_I 1 > Protein_J 1 > Protein_K 1 > Protein_L 1 > Protein_M 1 > POPC 451 > CHOL 0 > POPC 451 > CHOL 0 > W 60817 > NA+ 678 > CL- 671[/quote] > > where I did mistake? Does genbox reorent atom order in the -cp > waterSOLprot.gro -cs MEMBRANEsystem.gro ? Could it be fixed? > > 2016-04-18 16:21 GMT+02:00 James Starlight <jmsstarli...@gmail.com>: >> Ok thanks I will look into the tutorial! >> >> J. >> >> 2016-04-18 16:02 GMT+02:00 Kroon, P.C. <p.c.kr...@rug.nl>: >>> @Michael: Yes, you are right, a protein is a protein. IIRC the martinize >>> script does the same as pdb2gmx in this case. >>> @James: It really sounds like you want to do DAFT. >>> http://www.biotechnik.nat.uni-erlangen.de/research/boeckmann/downloads/DAFT/index.shtml >>> seems to contain an tutorial. Otherwise, consider contacting the author of >>> the paper (T Wassenaar). >>> >>> Peter >>> >>> On Mon, Apr 18, 2016 at 3:51 PM, Smith, Micholas D. <smit...@ornl.gov> >>> wrote: >>> >>>> Hi James, >>>> >>>> My guess is that running a two (unbound) protein simulation with the >>>> MARTINI force-field will be the same as if it was all atom. Build two >>>> separate protein topologies (with Martini force-fields) as *.itp files to >>>> include in your *.top and go from there. The topology file is what grompp >>>> uses to determine bonding, so if the topology file doesn't have the two >>>> proteins bound, they won't be. If I remember correctly, you can see an >>>> example (all-atom) topology file to work with if you use pdb2gmx for a pdb >>>> that contains 2 chains (with the proper flag the chains will be split). >>>> >>>> -Micholas >>>> >>>> =================== >>>> Micholas Dean Smith, PhD. >>>> Post-doctoral Research Associate >>>> University of Tennessee/Oak Ridge National Laboratory >>>> Center for Molecular Biophysics >>>> >>>> ________________________________________ >>>> From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se < >>>> gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of James >>>> Starlight <jmsstarli...@gmail.com> >>>> Sent: Monday, April 18, 2016 9:43 AM >>>> To: Discussion list for GROMACS users >>>> Subject: Re: [gmx-users] MARTINI simulation of protein-protein recognition >>>> >>>> It seems like smth very complicated :) >>>> >>>> I just need to put two different proteins in the system - one in the >>>> membrane (A) and one in the water (B) and simulate it independently 10 >>>> times to collect statistics about associations of A and B during those >>>> runs. The problems that I don't know how to put 2 different unbound >>>> proteins in the MARTINI system. >>>> >>>> James >>>> >>>> 2016-04-18 9:55 GMT+02:00 Kroon, P.C. <p.c.kr...@rug.nl>: >>>> > Hi, >>>> > >>>> > I assume you want to study the binding of your water soluble protein to >>>> > your membrane(protein). DAFT was created to do just this. DOI: >>>> > 10.1021/ct5010092 >>>> > >>>> > Peter >>>> > >>>> > On Fri, Apr 15, 2016 at 3:37 PM, James Starlight <jmsstarli...@gmail.com >>>> > >>>> > wrote: >>>> > >>>> >> Dear Gromacs users! >>>> >> >>>> >> I am looking for some tutorial for the MARTINI simulation of >>>> >> protein-protein recognition dealing with the big membrane protein >>>> >> simulated within the membrane and its assosiation with the small water >>>> >> soluble protein. The question - is it possible in existing Martini >>>> >> system conisdted of only membrane protein solvated in membrane with >>>> >> water to >>>> >> i) increase box size on Z >>>> >> ii)add some water >>>> >> iii) put another water soluble protein in new space (on the distance >>>> >> of the initial membrane protein complex) >>>> >> iv) edit topology of new system and run new md >>>> >> >>>> >> assuming that i,ii and iv are trivial the problem here is the iii step >>>> :-) >>>> >> >>>> >> or alternatively if I would like to run new simulation with those 2 >>>> >> proteins (in the unbound form) how I can prepare such complex system >>>> >> consisted of big protein in membrane plus water soluble protein >>>> >> unbound from it? >>>> >> >>>> >> Thanks! >>>> >> >>>> >> Gleb >>>> >> -- >>>> >> Gromacs Users mailing list >>>> >> >>>> >> * Please search the archive at >>>> >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before >>>> >> posting! >>>> >> >>>> >> * Can't post? 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