On 11/4/19 9:05 AM, daniel depope wrote:
I want to simulate POPE/POPG bilayer with gromos54a7 ff (expanded with lipids parts, as explained in Lemkul's kalp tutorial). 1. I tried CHARMM-gui website - I got bilayer in step 5, but can't finalize because there are no gromos ff option. So I looked for pope and popg gromos54a7 topology, but with no succes so I stacked. Any suggestions how to proceed?
CHARMM-GUI is intended for use with the CHARMM force field, so this is to be expected.
2. Another option was to build that bilayer with packmol, but I can't find a way to do so (I know how to build homogenuos bilayer). 3. POPE molecule from CHARMM-gui website have 125 atoms. I have some old POPE molecule with only 52 atoms. Last one has only two hydrogen atoms. Can anyone explain why is that a case.
CHARMM is an all-atom force field. GROMOS is united-atom. -Justin -- ================================================== Justin A. Lemkul, Ph.D. Assistant Professor Office: 301 Fralin Hall Lab: 303 Engel Hall Virginia Tech Department of Biochemistry 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.
