Hi Nickya, The masses have never been optimized, because we only parametrized equilibrium properties. You shouldn't look at dynamics with these CG models anyway.
The NAP and CAP groups are terminal side chains. See our JCP14 paper or my PhD thesis. Also, many of the bonds are the same by design, not by mistake. We built the model to have identical geometries for most residues to reproduce the same Ramachandran plots. It helped the optimization procedure. More details in Bereau and Deserno, JCP 2009. Best, Tristan On Thu, Oct 22, 2015 at 10:58 <[email protected]> wrote: > > Hello,all > > In VOTCA Tutorial website http://www.votca.org/tutorials/coarse-graining > > > <https://lh3.googleusercontent.com/-Q8HvFIRDXV4/Viie7EM8VMI/AAAAAAAAAAM/JBTDrWfKPkI/s1600/1.JPG> > > > > > > > Then, I downloaded "plumx" package, which is used for PLUM force field in > GROMACS. > There is a "plum.itp" file in the package. > I really wonder its correctness. > The mass of H is 10.00 ? > The mass of amino acid presented in the itp file is the mass of whole > amino acid, rather than the mass of side chain ? > What is the CAP with mass 75 ? > b0 and kb in different bond are almost same ? *[bondtypes]* > > *; PLUM force field* > > *;* > > *; Tristan Bereau, Aug. 1, 2011* > > *;* > > *; Please cite: * > > *;* > > *; T. Bereau and M. Deserno, J. Chem. Phys, 130, 235106 (2009)* > > *; Z.-J. Wang and M. Deserno, J. Phys. Chem. B 114, 11207 (2010).* > > > > *[ defaults ]* > > *;nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ* > > * 1 1 no 0.0 0.0* > > > *[ atomtypes ]* > > *; * > > *;type mass charge ptype V(C6) W(C12)* > > *; backbone* > > * HBN 14.00 0.000 A 0.000000000 0.000000000* > > * H 10.00 0.000 A 0.000000000 0.000000000* > > * CA 12.00 0.000 A 0.000000000 0.000000000* > > * HBC 12.00 0.000 A 0.000000000 0.000000000* > > * O 16.00 0.000 A 0.000000000 0.000000000* > > * N 14.00 0.000 A 0.000000000 0.000000000; > proline amide* > > *; sidechain C_beta beads* > > * ALA 89.0 0.000 A 0.000000000 0.000000000* > > * ARG0 174.0 0.000 A 0.000000000 0.000000000* > > * ARGP 174.0 0.000 A 0.000000000 0.000000000* > > * ASN 132.0 0.000 A 0.000000000 0.000000000* > > * ASP0 133.0 0.000 A 0.000000000 0.000000000* > > * ASPM 133.0 0.000 A 0.000000000 0.000000000* > > * CYS 121.0 0.000 A 0.000000000 0.000000000* > > * GLN 146.0 0.000 A 0.000000000 0.000000000* > > * GLU0 147.0 0.000 A 0.000000000 0.000000000* > > * GLUM 147.0 0.000 A 0.000000000 0.000000000* > > * GLY 75.0 0.000 A 0.000000000 0.000000000* > > * HIS 155.0 0.000 A 0.000000000 0.000000000* > > * ILE 131.0 0.000 A 0.000000000 0.000000000* > > * LEU 131.0 0.000 A 0.000000000 0.000000000* > > * LYS0 146.0 0.000 A 0.000000000 0.000000000* > > * LYSP 146.0 0.000 A 0.000000000 0.000000000* > > * MET 149.0 0.000 A 0.000000000 0.000000000* > > * PHE 165.0 0.000 A 0.000000000 0.000000000* > > * PRO 115.0 0.000 A 0.000000000 0.000000000* > > * SER 105.0 0.000 A 0.000000000 0.000000000* > > * THR 119.0 0.000 A 0.000000000 0.000000000* > > * TRP 204.0 0.000 A 0.000000000 0.000000000* > > * TYR 181.0 0.000 A 0.000000000 0.000000000* > > * VAL 117.0 0.000 A 0.000000000 0.000000000* > > * CAP 75.0 0.000 A 0.000000000 0.000000000; end > cap* > > *; lipid* > > * CH 87.166 0.0 A 0.000000 1.000000* > > * PH 94.970 0.0 A 0.000000 1.000000* > > * GL 41.073 0.0 A 0.000000 1.000000* > > * E1 58.036 0.0 A 0.000000 1.000000* > > * E2 58.036 0.0 A 0.000000 1.000000* > > * AS 42.081 0.0 A 0.000000 1.000000* > > * AD 26.038 0.0 A 0.000000 1.000000* > > * AE 29.062 0.0 A 0.000000 1.000000* > > > *[ bondtypes ]* > > *; i j func b0 kb* > > * HBN H 1 1.00000e-01 7.74000e+04* > > * HBN CA 1 1.45500e-01 7.74000e+04* > > * CA ALA 1 1.53000e-01 7.74000e+04* > > * CA ARG0 1 1.53000e-01 7.74000e+04* > > * CA ARGP 1 1.53000e-01 7.74000e+04* > > * CA ASN 1 1.53000e-01 7.74000e+04* > > * CA ASP0 1 1.53000e-01 7.74000e+04* > > * CA ASPM 1 1.53000e-01 7.74000e+04* > > * CA CYS 1 1.53000e-01 7.74000e+04* > > * CA GLN 1 1.53000e-01 7.74000e+04* > > * CA GLU0 1 1.53000e-01 7.74000e+04* > > * CA GLUM 1 1.53000e-01 7.74000e+04* > > * CA GLY 1 1.53000e-01 7.74000e+04* > > * CA HIS 1 1.53000e-01 7.74000e+04* > > * CA ILE 1 1.53000e-01 7.74000e+04* > > * CA LEU 1 1.53000e-01 7.74000e+04* > > * CA LYS0 1 1.53000e-01 7.74000e+04* > > * CA LYSP 1 1.53000e-01 7.74000e+04* > > * CA MET 1 1.53000e-01 7.74000e+04* > > * CA PHE 1 1.53000e-01 7.74000e+04* > > * CA PRO 1 1.53000e-01 7.74000e+04* > > * CA SER 1 1.53000e-01 7.74000e+04* > > * CA THR 1 1.53000e-01 7.74000e+04* > > * CA TRP 1 1.53000e-01 7.74000e+04* > > * CA TYR 1 1.53000e-01 7.74000e+04* > > * CA VAL 1 1.53000e-01 7.74000e+04* > > * CA CAP 1 1.53000e-01 7.74000e+04* > > * CA HBC 1 1.51000e-01 7.74000e+04* > > * HBC O 1 1.23500e-01 7.74000e+04* > > * HBC HBN 1 1.32500e-01 7.74000e+04* > > * N H 1 1.00000e-01 7.74000e+04* > > * N CA 1 1.45500e-01 7.74000e+04* > > * HBC N 1 1.32500e-01 7.74000e+04* > > *; lipids* > > * CH PH 8 1 1.0* > > * PH GL 8 2 1.0* > > * GL E1 8 3 1.0* > > * GL E2 8 4 1.0* > > * E1 AS 8 5 1.0* > > * E2 AS 8 6 1.0* > > * AS AS 8 7 1.0* > > * AS AD 8 8 1.0* > > * AS AE 8 9 1.0* > > *; efective angles* > > * CH GL 9 10 1.0 ;CH-PH-GL* > > * PH E1 9 11 1.0 ;PH-GL-E1* > > * PH E2 9 12 1.0 ;PH-GL-E2* > > * E1 E2 9 13 1.0 ;E1-GL-E2* > > * E1 AS 9 14 1.0 ;E1-AS-AS* > > * E2 AS 9 15 1.0 ;E2-AS-AS* > > * AS AS 9 16 1.0 ;AS-AS-AS* > > * AS AE 9 17 1.0 ;AS-AS-AE* > > * AS AD 9 21 1.0 ;AS-AS-AD* > > > > > Thanks in advance ! > Nickya > > -- > You received this message because you are subscribed to the Google Groups > "votca" group. > To unsubscribe from this group and stop receiving emails from it, send an > email to [email protected]. > To post to this group, send email to [email protected]. > Visit this group at http://groups.google.com/group/votca. > For more options, visit https://groups.google.com/d/optout. > -- You received this message because you are subscribed to the Google Groups "votca" group. To unsubscribe from this group and stop receiving emails from it, send an email to [email protected]. To post to this group, send email to [email protected]. Visit this group at http://groups.google.com/group/votca. For more options, visit https://groups.google.com/d/optout.
