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.
