Hi Justin, I have stumbled upon another problem. The sphingomyelin topology (PSM.itp) that Charmm-GUI provides has an atomtype called NHL that is not defined by the Charmm36 ff. I am using the latest charmm36-jun2015.ff. Could you please look in to this?
On Fri, Jan 22, 2016 at 4:29 PM, Ganesh Shahane <ganesh7shah...@gmail.com> wrote: > Thank you for your reply Justin!. It was helpful. > > On Fri, Jan 22, 2016 at 2:41 PM, Justin Lemkul <jalem...@vt.edu> wrote: > >> >> >> On 1/22/16 8:51 AM, Ganesh Shahane wrote: >> >>> Dear Gromacs users, >>> >>> I wish to simulate a mixed lipid bilayer of which one of the lipids is >>> sphingomyelin (PSM, 18:1-sphingosine and 16:0-palmitic acid) using >>> Charmm36 >>> ff. Towards this, I constructed the bilayer using Charmm-GUI but then was >>> surprised to find that its topology is not present in residue topology >>> database of Charmm36 ff. >>> >>> Does anyone has any idea about where can I get topology for PSM? Or would >>> it be wise to submit it to paramchem to get its topology? >>> >>> >> Use the force field CHARMM-GUI provides you. It supports everything in >> your system. Our charmm36.ff port may not include everything; I extend it >> only when people ask for specific parameters (as CHARMM is a huge force >> field, sometimes things get missed and I rely on this kind of feedback). >> I'll add sphingomyelin in the next release. >> >> -Justin >> >> -- >> ================================================== >> >> Justin A. Lemkul, Ph.D. >> Ruth L. Kirschstein NRSA Postdoctoral Fellow >> >> Department of Pharmaceutical Sciences >> School of Pharmacy >> Health Sciences Facility II, Room 629 >> University of Maryland, Baltimore >> 20 Penn St. >> Baltimore, MD 21201 >> >> jalem...@outerbanks.umaryland.edu | (410) 706-7441 >> http://mackerell.umaryland.edu/~jalemkul >> >> ================================================== >> -- >> 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. >> > > > > -- > Best Regards, > Ganesh Shahane > -- Best Regards, Ganesh Shahane -- 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.
