Dear users, I try to simualte PKAC with 1 Mg and ADP (4ntt.pdb).For PKAC and Mg topology I use the GROMACS-2016.3 AMBER99SB-ILDN. For ADP I try to use acpype. The H were assigned with pymol, only getting one at the phosphate groups what should be ok.Nevertheless acpype assigns the same paramters to the P-O single and P=O duoble bonds. acpype topology output: [ bonds ] ; ai aj funct r k 1 4 1 1.6020e-01 2.8660e+05 ; PA - O5' 1 13 1 1.4810e-01 4.0811e+05 ; PA - O1A 1 16 1 1.4810e-01 4.0811e+05 ; PA - O2A 1 19 1 1.6020e-01 2.8660e+05 ; PA - O3A 2 14 1 1.6250e-01 2.6878e+05 ; PB - O1B 2 17 1 1.4810e-01 4.0811e+05 ; PB - O2B 2 19 1 1.6020e-01 2.8660e+05 ; PB - O3A 2 20 1 1.4810e-01 4.0811e+05 ; PB - O3B 3 4 1 1.4390e-01 2.5230e+05 ; C5' - O5'
This is what the structure looks like (projected to 2D): H - O1B O1A | || O3B - PB - O3A - PA - O5' - C5' - ... || | O2B O2A The paramters should also depend on the bond type so I am not sure if this output is right. In the input .mol2 file the double bonds are assigned like in the structure above.Pymol shows only single bonds investigating the acpype output. So what can I do to assign the double bonds correctly. Is it possible with acpype? Or doens't it matter? Thanks for your help! Best regards,olaf -- 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.
