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.
