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bay__gulf金虫 (著名写手)
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【在线答疑】关于NAMD/VMD 已有27人参与
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小木虫(金币+0.5):给个红包，谢谢回帖交流
小木虫(金币+0.5):给个红包，谢谢回帖交流
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为什么自动产生的参数文件没有内容呢？ 像下边： !>>>>>> Combined CHARMM All-Hydrogen Parameter File for <<<<<<<<< !>>>>>>>>> CHARMM22 Proteins and CHARMM27 Lipids <<<<<<<<<< !from !>>>> CHARMM22 All-Hydrogen Parameter File for Proteins <<<<<<<<<< !>>>>>>>>>>>>>>>>>>>>>> August 1999 <<<<<<<<<<<<<<<<<<<<<<<<<<<<< !>>>>>>> Direct comments to Alexander D. MacKerell Jr. <<<<<<<<< !>>>>>> 410-706-7442 or email: alex,mmiris.ab.umd.edu <<<<<<<<< !and ! \\\ CHARMM27 All-Hydrogen Lipid Parameter File /////// ! \\\\\\\\\ Developmental ///////////////////////// ! Alexander D. MacKerell Jr. ! August 1999 ! All comments to ADM jr. email:alex,mmiris.ab.umd.edu ! telephone: 410-706-7442 ! ! +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ ! + Residue topologies/parameters generated by PARATOOL. + ! + + ! + PARATOOL is an interactive tool for generation of force field parameters. + ! + and can be obtained free of charge from + ! + http://bioinf.charite.de/biophys/paratool + ! + + ! + Author: + ! + Jan Saam + ! + Institute of Biochemistry + ! + Charite Berlin + ! + Germany + ! + saam@charite.de + ! + + ! + CITATION: + ! + If you use PARATOOL or topologies/parameters generated by this program, + ! + please cite the following work: + ! + Saam, et al. (2006), ... + ! +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ ! Parameters for components GLY THR ! To be used in combination with: ! F://20090703/par_all27_prot_lipid.inp BONDS ! !V(bond) = Kb(b - b0)**2 ! !Kb: kcal/mole/A**2 !b0: A ! !atom type Kb b0 ! ANGLES ! !V(angle) = Ktheta(Theta - Theta0)**2 ! !V(Urey-Bradley) = Kub(S - S0)**2 ! !Ktheta: kcal/mole/rad**2 !Theta0: degrees !Kub: kcal/mole/A**2 (Urey-Bradley) !S0: A ! !atom types Ktheta Theta0 Kub S0 ! DIHEDRALS ! !V(dihedral) = Kchi(1 + cos(n(chi) - delta)) ! !Kchi: kcal/mole !n: multiplicity !delta: degrees ! !atom types Kchi n delta ! IMPROPER ! !V(improper) = Kpsi(psi - psi0)**2 ! !Kpsi: kcal/mole/rad**2 !psi0: degrees !note that the second column of numbers (0) is ignored ! !atom types Kpsi 0 psi0 ! NONBONDED nbxmod 5 atom cdiel shift vatom vdistance vswitch - cutnb 14.0 ctofnb 12.0 ctonnb 10.0 eps 1.0 e14fac 1.0 wmin 1.5 !adm jr., 5/08/91, suggested cutoff scheme ! !V(Lennard-Jones) = Eps(i,j)*[(Rmin(i,j)/r(i,j))**12 - 2(Rmin(i,j)/r(i,j))**6] ! !epsilon [kcal/mole]: Eps(i,j) = sqrt(eps(i) * eps(j)) !Rmin/2 [A]: Rmin(i,j) = Rmin/2(i) + Rmin/2(j) ! !atom ignored epsilon Rmin/2 ignored eps,1-4 Rmin/2,1-4 ! END |
24楼2009-07-03 15:14:56
2楼2009-05-02 11:58:42
bay__gulf
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lei0736(金币+4,VIP+0):谢谢 又添猛将 5-3 16:09
lei0736(金币+4,VIP+0):谢谢 又添猛将 5-3 16:09
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【回2楼】 可以，比如下面这篇文献 Bryan J. Johnson, Jordi Cohen, Richard W. Welford, Arwen R. Pearson, Klaus Schulten, Judith P. Klinman, and Carrie M. Wilmot. Exploring molecular oxygen pathways in Hanseluna Polymorpha copper-containing amine oxidase. Journal of Biological Chemistry, 282:17767-17776, 2007. [ Last edited by bay__gulf on 2009-5-2 at 13:21 ] |
3楼2009-05-02 13:13:06
4楼2009-05-02 13:45:28