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.
