Hi. I'm quite new to molecular dynamics too. How did you make that itp? Does your system contain only one protein/DNA molecule?
May be try this tutorial for a single protein? http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/ Check multiple journal papers when you decide how to simulate (even if you are just simulating a single small protein). Some systems might need different simulation steps. And, depending on the things that you want to look at, you might have to stage a different simulation. On Sat, Dec 13, 2014 at 1:46 PM, Devender Arora <devar...@hotmail.com> wrote: > > I am facing a problem in Gromacs while running grommp please do give the > right direction I am new to Molecular dynamics. > > > Fatal error: > Syntax error - File topol_Protein_chain_A.itp, line 6966 > Last line read: > '[ molecules ]' > Invalid order for directive molecules > For more information and tips for troubleshooting, please check the GROMACS > website at http://www.gromacs.org/Documentation/Errors > > : > > > Thanks & Regards > > > Devender Arora > > > Ph.D Scholar > > > Department of Biotechnology > > > GB Pant engineering College > > > Pauri Garhwal, Uttarakhand > > > Contact No. +919720045608, +91986896786 > > > -- > 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.