Dear Justin, Why there are 6 equilibrations MDP's generated and how could I use one? Which one should be opted for?
I found a Readme python script and is that one should be executed it? Thank you On Tue, Apr 10, 2018 at 11:53 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 4/10/18 2:21 PM, RAHUL SURESH wrote: > >> Dear Users, >> >> Performing membrane simulations using charmm36 ff. The Protein/membrane >> system is constructed using charmm-gui [POPC] . The system was then used >> in >> gromacs 2016.4 for simulation . Following the simulation tutorial, >> >> *gmx pdb2gmx -f KALP-15_princ.pdb -o KALP-15_processed.gro -ignh -ter >> -water spc* >> > > You shouldn't be doing this. CHARMM should not be used with SPC, and in > fact if you built the system with CHARMM-GUI you have all the topologies > and input files necessary to proceed directly with energy minimization, > equilibration, etc. > > -Justin > > NH2 and COOH were chosen as terminals. >> >> But bad luck its shows a fatal error. >> >> *fatal error:* >> *There were 49308 missing atoms in molecule Protein if you want to use >> this* >> *incomplete topology anyhow, use the option -missing* >> >> All the missing atoms were only hydrogen. >> >> the water model was then changed to tip3p, even the error prevails. >> >> Why the ignh flag doesn't work here? >> Can I go with -missing? >> >> Thank you >> >> > -- > ================================================== > > Justin A. Lemkul, Ph.D. > Assistant Professor > Virginia Tech Department of Biochemistry > > 303 Engel Hall > 340 West Campus Dr. > Blacksburg, VA 24061 > > jalem...@vt.edu | (540) 231-3129 > http://www.thelemkullab.com > > ================================================== > > -- > 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. > -- *Regards,* *Rahul Suresh* *Research Scholar* *Bharathiar University* *Coimbatore* -- 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.