2015-10-22 2:58 GMT-06:00 <[email protected]>: > > 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. > The url were a bit outdated. Plumx can now be found here: <https://github.com/tbereau/plumx> The files interesting for VOTCA are here: <https://github.com/tbereau/plumx/tree/master/dppc_mapping>
> 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]* > These questions are related to the plum model not VOTCA, so ask them on the plum-x mailing list ([email protected], CC'ed) > *; 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. > -- Christoph Junghans Web: http://www.compphys.de -- 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.
