Thanks for your response. First of all I must say it is a bit strange that OPLS has the atom types of phenyl ester but not the corresponding dihedral angels to support it. But I see your point but could you elaborate on how I could evaluate this? How can I calculate those profiles?
Thanks, Max On Jun 7, 2015, at 9:49 AM, Justin Lemkul <[email protected]<mailto:[email protected]>> wrote: On 6/5/15 6:08 PM, Ebert Maximilian wrote: Hi, a small little update. I saw that CT OS C_2 O_2 and CT OS C_2 CT are defined OPLS/AA. I used these parameters now to define CA OS C_2 O_2 and CA OS C_2 CT in OPLS/AA. Any thoughts on that? I really have difficulties to visualize dihedral angles and I am not sure if this would actually give roughly the same geometry or not. The determining factor is whether or not the QM and MM energy profiles match as those dihedrals are rotated. -Justin Thanks and have a good weekend. Max On Jun 5, 2015, at 4:38 PM, Ebert Maximilian <[email protected]<mailto:[email protected]>> wrote: Dear list, I ran into some problem to define the topology of phenyl palmitate. My main problem is a missing dihedral angle definition in OPLS/AA. Here is a sketch of the molecule without hydrogen (I hope it turns out to be readable in the email): O17 || C21 - C20 C16 (C)n / \ / \ / \ C22 C19 - O18 C15 C1 \ / C23 - C24 I think I defined the atom types correctly: [ atoms ] ; nr type resi res atom cgnr charge mass 1 opls_768 1 PNR C22 4 -0.1952 12.01100 2 opls_145 1 PNR C21 5 -0.0500 12.01100 3 opls_145 1 PNR C20 6 -0.1550 12.01100 4 opls_145 1 PNR C23 7 -0.0500 12.01100 5 opls_145 1 PNR C24 8 -0.1550 12.01100 6 opls_472 1 PNR C19 9 0.1591 12.01100 7 opls_473 1 PNR O18 10 -0.3732 15.99940 8 opls_465 1 PNR C16 11 0.6491 12.01100 9 opls_466 1 PNR O17 12 -0.5100 15.99940 10 opls_136 1 PNR C15 13 -0.1264 12.01100 11 opls_136 1 PNR C14 14 -0.0804 12.01100 12 …. The problem is now in the ester since there is no dihedral definition of CA OS C_2 O_2 and CA OS C_2 CT in OPLS/AA. I assigned C19 the atom type 472 which is Cipso phenyl ester with type CA and hence O18 473 (AA -OR phenyl ester). Do I understand 472 correctly? How can I resolve the missing two dihedral angles? I also wanted to know if somebody has an idea what is meant by: AA C: esters - for R on C=O, use #280-#282 of the atom type opls_465. Do I need in this case to assign opls_280 to C15 and opls_282 to the corresponding hydrogens since they are the R of the ester? Thank you very much for your advice, Max -- 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 [email protected]<mailto:[email protected]>. -- ================================================== 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 [email protected]<mailto:[email protected]> | (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 [email protected]<mailto:[email protected]>. -- 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 [email protected].
