Create index group that have both protein and ACO. gmx make_ndx will serve this task. Then create a pdb file file from gmx trjconv Or you can choose system as output and delete ions and solvent from any editor.
On Mon, Apr 24, 2017 at 3:21 PM, abhisek Mondal <abhisek.m...@gmail.com> wrote: > Hello, > > Alright. I have tried this but I'm stuck in the following scenario. > I'm using trjconv for getting pdb file of the protein-ligand complex (used > for umbrella sampling). > trjconv_mpi -f confout1.gro -o conf_1.pdb -n index.ndx -s npt.tpr > > This is giving me the following prompt: > Select group for output > Group 0 ( System) has 27051263 elements > Group 1 ( Protein) has 1588 elements > Group 2 ( Protein-H) has 1245 elements > Group 3 ( C-alpha) has 158 elements > Group 4 ( Backbone) has 474 elements > Group 5 ( MainChain) has 633 elements > Group 6 ( MainChain+Cb) has 784 elements > Group 7 ( MainChain+H) has 785 elements > Group 8 ( SideChain) has 803 elements > Group 9 ( SideChain-H) has 612 elements > Group 10 ( Prot-Masses) has 1588 elements > Group 11 ( non-Protein) has 27049675 elements > Group 12 ( Other) has 59 elements > Group 13 ( ACO) has 59 elements > Group 14 ( NA) has 16615 elements > Group 15 ( CL) has 16615 elements > Group 16 ( Water) has 27016386 elements > Group 17 ( SOL) has 27016386 elements > Group 18 ( non-Water) has 34877 elements > Group 19 ( Ion) has 33230 elements > Group 20 ( ACO) has 59 elements > Group 21 ( NA) has 16615 elements > Group 22 ( CL) has 16615 elements > Group 23 ( Water_and_ions) has 27049616 elements > Group 24 ( > > Now how can I be able to get both Protein+ACO as a pdb file ? > If I could get Protein+ACO, then I could strip the box size for further > umbrella sampling procedure. > > However, is it possible to go with the following way: > editconf_mpi -f confout1.gro -o conf_1.gro -c -d 1.0 -bt cubic > > Please suggest me a way. > > Thank you. > > On Mon, Apr 24, 2017 at 1:38 AM, Mark Abraham <mark.j.abra...@gmail.com> > wrote: > > > Hi, > > > > Take a configuration of interest, strip the solvent, put it in a box you > > think is good, and re-equilibrate just like you did before you started. > > > > Mark > > > > On Sun, Apr 23, 2017 at 8:59 PM abhisek Mondal <abhisek.m...@gmail.com> > > wrote: > > > > > Hi, > > > > > > Yes, I did when I started the simulation. The box size I used to start > > the > > > simulation was very big(I was dealing with an unknown sample). After > > > successfully generating the configurations I realized that further work > > > could move faster if I could trim the box size little bit now. > > > So is there any way now to reduce the box size and proceed with > relevant > > > configurations towards PMF generation ? > > > Please suggest me a way here. > > > > > > Thank you. > > > > > > On Apr 24, 2017 12:22 AM, "Mark Abraham" <mark.j.abra...@gmail.com> > > wrote: > > > > > > > Hi, > > > > > > > > You get to choose the box size eg with editconf when you set up your > > > > simulation. It's not pre-defined ;-) > > > > > > > > Mark > > > > > > > > On Sun, 23 Apr 2017 20:28 abhisek Mondal <abhisek.m...@gmail.com> > > wrote: > > > > > > > > > Hello, > > > > > > > > > > Another thing I wanted to ask. > > > > > After generating configurations I found out that the predefined box > > > size > > > > > (used to reach so far) is excessively high. > > > > > Is it possible to trim the box size to perform further mdrun during > > > > > umbrella sampling? > > > > > > > > > > Please suggest me a way, it is taking very long time with current > box > > > > size. > > > > > > > > > > Thank you. > > > > > > > > > > > > > > > > > > > > On Apr 23, 2017 10:02 PM, "Mark Abraham" <mark.j.abra...@gmail.com > > > > > > wrote: > > > > > > > > > > > Hi, > > > > > > > > > > > > You can only load a trajectory with fewer frames. Either don't > > write > > > so > > > > > > many, or filter it with trjconv first. > > > > > > > > > > > > Mark > > > > > > > > > > > > On Sun, 23 Apr 2017 17:20 abhisek Mondal <abhisek.m...@gmail.com > > > > > > wrote: > > > > > > > > > > > > > Hi, > > > > > > > I'm having a problem loading trajectory file after umbrella > > > sampling. > > > > > The > > > > > > > file is so huge in size that the VMD finally runs out of > memory. > > > I'm > > > > > > > operating with 125gb of physical memory here though. > > > > > > > > > > > > > > Is there any way out of it ? > > > > > > > > > > > > > > > > > > > > > Thank you > > > > > > > -- > > > > > > > Abhisek Mondal > > > > > > > > > > > > > > *Senior Research Fellow* > > > > > > > > > > > > > > *Structural Biology and Bioinformatics Division* > > > > > > > *CSIR-Indian Institute of Chemical Biology* > > > > > > > > > > > > > > *Kolkata 700032* > > > > > > > > > > > > > > *INDIA* > > > > > > > -- > > > > > > > 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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Read http://www.gromacs.org/Support/Mailing_Lists > > > > * For (un)subscribe requests visit > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > > send a mail to gmx-users-requ...@gromacs.org. > > > > > > -- > Abhisek Mondal > > *Senior Research Fellow* > > *Structural Biology and Bioinformatics Division* > *CSIR-Indian Institute of Chemical Biology* > > *Kolkata 700032* > > *INDIA* > -- > Gromacs Users mailing list > > * Please search the archive at http://www.gromacs.org/ > Support/Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- 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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