[gmx-users] Problem - How to center a protein in a CG simulation
Carlos Navarro Retamal
cnavarro at utalca.cl
Mon Nov 10 18:18:29 CET 2014
Dear Tsjerk,
I don’t understand what you mean.
Take a look at the next image.
http://cl.ly/262g2q2C2o3H
You say this is ok? Even when i open the file with vmd i got tons of warning message:
> Warning) Unusual bond between residues: 44 (protein) and 45 (none)
> Warning) Unusual bond between residues: 45 (none) and 46 (protein)
> Warning) Unusual bond between residues: 47 (protein) and 48 (none)
> Warning) Unusual bond between residues: 49 (none) and 50 (protein)
> Warning) Unusual bond between residues: 60 (none) and 61 (protein)
> Warning) Unusual bond between residues: 62 (protein) and 63 (none)
> Warning) Unusual bond between residues: 63 (none) and 64 (protein)
> Warning) Unusual bond between residues: 66 (protein) and 67 (none)
> Warning) Unusual bond between residues: 70 (protein) and 71 (none)
> Warning) Unusual bond between residues: 71 (none) and 72 (protein)
> Warning) Unusual bond between residues: 91 (none) and 92 (protein)
> Warning) Unusual bond between residues: 99 (protein) and 100 (none)
> Warning) Unusual bond between residues: 101 (none) and 102 (protein)
> Warning) Unusual bond between residues: 102 (protein) and 103 (none)
> Warning) Unusual bond between residues: 103 (none) and 104 (protein)
> Warning) Unusual bond between residues: 110 (protein) and 111 (none)
> Warning) Unusual bond between residues: 111 (none) and 112 (protein)
> Warning) Unusual bond between residues: 113 (protein) and 114 (none)
> Warning) Unusual bond between residues: 120 (none) and 121 (protein)
> Warning) Unusual bond between residues: 122 (protein) and 123 (none)
> Warning) Unusual bond between residues: 123 (none) and 124 (protein)
> Warning) Unusual bond between residues: 124 (protein) and 125 (none)
> Warning) Unusual bond between residues: 125 (none) and 126 (protein)
> Warning) Unusual bond between residues: 126 (protein) and 127 (none)
> Warning) Unusual bond between residues: 128 (none) and 129 (protein)
> Warning) Unusual bond between residues: 130 (protein) and 131 (none)
> Warning) Unusual bond between residues: 131 (none) and 132 (protein)
> Warning) Unusual bond between residues: 134 (protein) and 135 (none)
> Warning) Unusual bond between residues: 135 (none) and 136 (protein)
> Warning) Unusual bond between residues: 211 (protein) and 212 (none)
> Warning) Unusual bond between residues: 212 (none) and 213 (protein)
> Warning) Unusual bond between residues: 226 (protein) and 227 (none)
> Warning) Unusual bond between residues: 227 (none) and 228 (protein)
> Warning) Unusual bond between residues: 247 (protein) and 248 (none)
> Warning) Unusual bond between residues: 248 (none) and 249 (protein)
> Warning) Unusual bond between residues: 16 (protein) and 17 (none)
> Warning) Unusual bond between residues: 17 (none) and 18 (protein)
> Warning) Unusual bond between residues: 18 (protein) and 19 (none)
> Warning) Unusual bond between residues: 20 (none) and 21 (protein)
> Warning) Unusual bond between residues: 77 (protein) and 78 (none)
> Warning) Unusual bond between residues: 78 (none) and 79 (protein)
> Warning) Unusual bond between residues: 81 (protein) and 82 (none)
> Warning) Unusual bond between residues: 82 (none) and 83 (protein)
> Warning) Unusual bond between residues: 84 (protein) and 85 (none)
> Warning) Unusual bond between residues: 85 (none) and 86 (protein)
> Warning) Unusual bond between residues: 123 (protein) and 124 (none)
> Warning) Unusual bond between residues: 126 (none) and 127 (protein)
> Warning) Unusual bond between residues: 140 (protein) and 141 (none)
> Warning) Unusual bond between residues: 141 (none) and 142 (protein)
> Warning) Unusual bond between residues: 143 (protein) and 144 (none)
> Warning) Unusual bond between residues: 144 (none) and 145 (protein)
> Warning) Unusual bond between residues: 155 (protein) and 156 (none)
> Warning) Unusual bond between residues: 156 (none) and 157 (protein)
> Warning) Unusual bond between residues: 207 (none) and 208 (protein)
> Warning) Unusual bond between residues: 242 (protein) and 243 (none)
> Warning) Unusual bond between residues: 243 (none) and 244 (protein)
> Warning) Unusual bond between residues: 245 (protein) and 246 (none)
> Warning) Unusual bond between residues: 246 (none) and 247 (protein)
sorry for asking to much stuffs, but this is my first time trying to convert a system form a CG-representation to an AA one.
Thanks for all of your help.
Best Regards,
Carlos
--
Carlos Navarro Retamal
Bioinformatic engineer
Ph.D(c) in Applied Science, Universidad de Talca, Chile
Center of Bioinformatics and Molecular Simulations (CBSM)
Universidad de Talca
2 Norte 685, Casilla 721, Talca - Chile
Teléfono: 56-71-201 798,
Fax: 56-71-201 561
Email: carlos.navarro87 at gmail.com or cnavarro at utalca.cl
On Monday, November 10, 2014 at 2:11 PM, Tsjerk Wassenaar wrote:
> Hey :)
>
> The protein is a dimer. Are you sure there is a real problem?
>
> Cheers,
>
> Tsjerk
>
> On Mon, Nov 10, 2014 at 6:07 PM, Carlos Navarro Retamal <cnavarro at utalca.cl (mailto:cnavarro at utalca.cl)>
> wrote:
>
> > Dear Tsjerk,
> > I forgot to mention it, but indeed i used -pbc mol, as follows:
> >
> >
> > > trjconv -f dynamic-NO-Elastic.gro -s dynamic-NO-Elastic.tpr -pbc mol -o
> > LastFrame.gro
> > >
> >
> >
> > And using this file (LastFrame.gro) i run initram, getting my protein
> > split on different side of the box.
> > What could it be?
> > Best Regards,
> > Carlos
> > --
> > Carlos Navarro Retamal
> > Bioinformatic engineer
> > Ph.D(c) in Applied Science, Universidad de Talca, Chile
> > Center of Bioinformatics and Molecular Simulations (CBSM)
> > Universidad de Talca
> > 2 Norte 685, Casilla 721, Talca - Chile
> > Teléfono: 56-71-201 798,
> > Fax: 56-71-201 561
> > Email: carlos.navarro87 at gmail.com (mailto:carlos.navarro87 at gmail.com) or cnavarro at utalca.cl (mailto:cnavarro at utalca.cl)
> >
> >
> > On Monday, November 10, 2014 at 1:35 PM, Tsjerk Wassenaar wrote:
> >
> > > Hi Carlos,
> > >
> > > You used -pbc nojump on the last frame with the .tpr as reference, which
> > > means it removes the jumps with respect to the tpr, and that will give
> > > rubbish. You should use -pbc mol and try again.
> > >
> > > Cheers,
> > >
> > > Tsjerk
> > >
> > > On Mon, Nov 10, 2014 at 5:25 PM, Carlos Navarro Retamal <
> > cnavarro at utalca.cl (mailto:cnavarro at utalca.cl)>
> > > wrote:
> > >
> > > > Dear Erick,
> > > > First of all thanks a lot for your reply.
> > > > Your are correct. I know that there’s not a ‘middle’ part in the system
> > > > (based on the PBC), i was just trying to say that i need a structure
> > > >
> > >
> > >
> >
> > where
> > > > the protein will be surrounded by the POPC membrane in order to have
> > > > ‘valid’ structure to start the AA MD simulations.
> > > >
> > > > I run the following commands:
> > > >
> > > > > trjconv -f dynamic-NO-Elastic.gro -s dynamic-NO-Elastic.tpr -pbc
> > nojump
> > > > -o LastFrame.gro
> > > > >
> > > >
> > > >
> > > >
> > > >
> > > > followed by:
> > > >
> > > > > trjconv -f LastFrame.gro -s dynamic-NO-Elastic.tpr -fit rot+trans -o
> > > > conf.gro
> > > > >
> > > >
> > > >
> > > >
> > > > without luck ( the proteins is not fix either with these commands).
> > > > what should i do?
> > > >
> > > >
> > > > Dear Tsjerk,
> > > > Thanks for your kind reply.
> > > > I did what you suggested, without luck:
> > > > > ./initram.sh (http://initram.sh) -f LastFrame.gro -o
> > > >
> > > >
> > >
> >
> > aa_gromos54a7.gro -to gromos54a7 -p
> > > >
> > > > topol.top
> > > > (in the input file the protein is intact)
> > > > CG-model:
> > > > http://cl.ly/3V3E1O2R0L31
> > > > AA-model
> > > > http://cl.ly/0U2r2n0F290i
> > > >
> > > >
> > > > Thanks to both of you for all your help,
> > > > Best Regards,
> > > > Carlos
> > > >
> > > > --
> > > > Carlos Navarro Retamal
> > > > Bioinformatic engineer
> > > > Ph.D(c) in Applied Science, Universidad de Talca, Chile
> > > > Center of Bioinformatics and Molecular Simulations (CBSM)
> > > > Universidad de Talca
> > > > 2 Norte 685, Casilla 721, Talca - Chile
> > > > Teléfono: 56-71-201 798,
> > > > Fax: 56-71-201 561
> > > > Email: carlos.navarro87 at gmail.com (mailto:carlos.navarro87 at gmail.com)
> > > >
> > >
> >
> > or cnavarro at utalca.cl (mailto:cnavarro at utalca.cl)
> > > >
> > > >
> > > > On Monday, November 10, 2014 at 12:16 PM, Erik Marklund wrote:
> > > >
> > > > > Dear Carlos,
> > > > >
> > > > > I guess it's just not obvious to most of us why this is a problem at
> > > > all. If the protein diffuses (as proteins do) you can just
> > > >
> > >
> >
> > translate/rotate
> > > > it back to where it was. Strictly speaking , there is no 'middle' in a
> > > > periodic system. Or are we missing something?
> > > > >
> > > > > In any case, adding restraints can affect the dynamics and you can
> > often
> > > > use trjconv -nojump followed by trjconv -fit to get your protein sit
> > > > steadily in the middle of your box, assuming the protein was where you
> > > > wanted it to be in the first place.
> > > > >
> > > > > Kind regards,
> > > > > Erik
> > > > >
> > > > >
> > > > > Erik Marklund, PhD
> > > > > Postdoctoral Research Fellow, Fulford JRF
> > > > >
> > > > > Department of Chemistry
> > > > > Physical & Theoretical Chemistry Laboratory
> > > > > University of Oxford
> > > > > South Parks Road
> > > > > Oxford
> > > > > OX1 3QZ
> > > > >
> > > > > On 10 Nov 2014, at 15:01, Carlos Navarro Retamal <cnavarro at utalca.cl (mailto:cnavarro at utalca.cl)
> > (mailto:cnavarro at utalca.cl)
> > > > <mailto:cnavarro at utalca.cl>> wrote:
> > > > >
> > > > > nobody?
> > > > > if there is not a way to do this at this moment (after the
> > > > >
> > > >
> > > >
> > >
> >
> > simulation)
> > > > >
> > > >
> > > >
> > > > is there a way to apply a restraint to maintain fix the protein in the
> > > > middle of the POPC bilayer (other than elastic network) during the MD
> > > > simulation in order to avoid this problem?
> > > > > Best regards,
> > > > > Carlos
> > > > >
> > > > > --
> > > > > Carlos Navarro Retamal
> > > > > Bioinformatic engineer
> > > > > Ph.D(c) in Applied Science, Universidad de Talca, Chile
> > > > > Center of Bioinformatics and Molecular Simulations (CBSM)
> > > > > Universidad de Talca
> > > > > 2 Norte 685, Casilla 721, Talca - Chile
> > > > > Teléfono: 56-71-201 798,
> > > > > Fax: 56-71-201 561
> > > > > Email: carlos.navarro87 at gmail.com<mailto:carlos.navarro87 at gmail.com>
> > > > >
> > > >
> > > >
> > >
> >
> > or
> > > > >
> > > >
> > > >
> > > > cnavarro at utalca.cl<mailto:cnavarro at utalca.cl>
> > > > >
> > > > >
> > > > > On Monday, November 10, 2014 at 2:11 AM, Carlos Navarro Retamal
> > wrote:
> > > > >
> > > > > Dear gromacs users,
> > > > > I’m trying to replicate the following paper:
> > > > >
> > > >
> > >
> >
> > http://www.nature.com/ncomms/2014/140708/ncomms5377/full/ncomms5377.html
> > > > >
> > > > > On that way i:
> > > > > - Create a CG (two different ones, with and without elastic-network
> > > > >
> > > >
> > > >
> > > > restraints) representation of my K2P protein by using martinize.py
> > > > > - I embedded it in a POPC bilayer membrane using insane.py
> > > > > After some energy minimization and equilibration i run a 500ns MD of
> > > > >
> > > >
> > > >
> > > > production.
> > > > > The problem was that during both simulation the protein starts to
> > > >
> > > >
> > >
> >
> > move
> > > >
> > > > across the box to a different box.
> > > > > By using tryconv as follows:
> > > > > trjconv -f dynamic-NO-Elastic.gro -s dynamic-NO-Elastic.tpr -pbc mol
> > > > >
> > > >
> > > >
> > >
> >
> > -o
> > > > >
> > > >
> > > >
> > > > LastFrame.gro
> > > > >
> > > > >
> > > > > i was able to ‘fix’ the protein (fix the pbc issue of the protein),
> > but
> > > > its remains out of the box.
> > > > > I even used -center keyword without luck.
> > > > > And since i need a structure where the protein remains in the middle
> > > > >
> > > >
> > > >
> > >
> >
> > of
> > > > >
> > > >
> > > >
> > > > the POPC membrane in order to perform the ‘backward’ step to obtain an
> > AA
> > > > representation of my system and perform a new MD simulation i’m kind of
> > > > stuck.
> > > > > I don’t know what to do :/
> > > > > Hope someone can help me.
> > > > > Have a nice week,
> > > > > Carlos
> > > > >
> > > > >
> > > > > --
> > > > > Carlos Navarro Retamal
> > > > > Bioinformatic engineer
> > > > > Ph.D(c) in Applied Science, Universidad de Talca, Chile
> > > > > Center of Bioinformatics and Molecular Simulations (CBSM)
> > > > > Universidad de Talca
> > > > > 2 Norte 685, Casilla 721, Talca - Chile
> > > > > Teléfono: 56-71-201 798,
> > > > > Fax: 56-71-201 561
> > > > > Email: carlos.navarro87 at gmail.com<mailto:carlos.navarro87 at gmail.com>
> > > > >
> > > >
> > > >
> > > > (mailto:carlos.navarro87 at gmail.com) or cnavarro at utalca.cl (mailto:cnavarro at utalca.cl) (mailto:
> > cnavarro at utalca.cl (mailto:cnavarro at utalca.cl))<mailto:
> > > > cnavarro at utalca.cl> (mailto:cnavarro at utalca.cl)
> > > > >
> > > > > --
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> > > Tsjerk A. Wassenaar, Ph.D.
> > > --
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