Yea, I haven't. I should do that first. Thank you. On Wed, Apr 11, 2018 at 12:29 AM, Justin Lemkul <jalem...@vt.edu> wrote:
> > > On 4/10/18 2:58 PM, RAHUL SURESH wrote: > >> Dear Justin, >> >> Why there are 6 equilibrations MDP's generated and how could I use one? >> Which one should be opted for? >> > > All of them, in sequence, if you want to follow the recommended Membrane > Builder protocol (you should read that reference if you haven't already so > you know what the Membrane Builder is doing and what the equilibration > scheme actually does). > > -Justin > > > >> 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. >>> >>> >> >> > -- > ================================================== > > 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.
