Hi, Grompp is running successfully without any errors. But my protein and ligands are very far away from each other. So, what I fear is that the interactions among them may not be well accounted for by MD simulations.
On Mon, Aug 7, 2017 at 7:53 PM, Mark Abraham <mark.j.abra...@gmail.com> wrote: > Hi, > > The only thing that matters is the order of the molecules, residues and > atoms, and preferably naming. These must match between topology and > coordinates when you eg use grompp. The point of doing an MD simulation is > generally to keep the topology constant while changing the coordinates. So > give grompp whatever file in whatever format suits you, subject to the > above constraint. > > Mark > > On Mon, 7 Aug 2017 16:25 Souvik Dey <souvik.de...@gmail.com> wrote: > > > Hi, > > > > I am trying to simulate a Protein Ligand system. Now, my system has some > > non standard residues and I standardized them for AMBER forcefield using > > ACPYPE. However, when I assemble the gro files of the Proten generated > from > > pdb2gmx and the gro files obtained from ACPYPE, I see that they are not > > situated next to each other. They have have moved far away. > > > > Now, is there any trick by which the coordinates of the PDB file do not > > change while being converted into a gro file or is there any way to > restore > > the previous condition of the PDB file? > > > > Thanking you, > > Souvik Dey > > > > -- > > Souvik Dey > > Integrated Science Education & Research Centre > > Visva Bharati University > > Santiniketan-731235 > > West Bengal > > 8981736643 > > -- > > 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? 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. > -- Souvik Dey Integrated Science Education & Research Centre Visva Bharati University Santiniketan-731235 West Bengal 8981736643 -- 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.