Dear all, I am checking the itp file for my ligand obtained from prodrg beta, using gromos96.1 ff (43a1). In the [ dihedrals ] section, I found lines such as
; ai aj ak al fu c0, c1, m, ... 31 32 24 28 2 35.3 334.8 35.3 334.8 ; imp C4 N1 O1 C2 32 31 33 37 2 0.0 167.4 0.0 167.4 ; imp N1 C4 C12 C11 for tetrahedral centres and substituents of rings, respectively, that make sense, but also 32 33 35 36 2 0.0 209.3 0.0 209.3 ; imp N1 C12 N2 C13 for out-of-plane bending, for which I don't see where the force value (209.3) come from. From the ffG43a1bon.itp file, there are only 3 improper types: #define gi_1 0.0 167.42309 ; planar groups 40 ; #define gi_2 35.26439 334.84617 ; tetrahedral centres 80 ; #define gi_3 0.0 669.69235 ; heme iron 160 Can someone explain how prodrg get the value for the force constant for out-of-plane bending of rings? Also, what is meaning of the (commented) values 40, 80 and 160 in this excerpt of ffG43a1bon.itp? Many thanks, Rui Rodrigues -- Webmail ESTG de Leiria (http://webmail.estg.ipleiria.pt) _______________________________________________ gmx-users mailing list [email protected] http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
