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易风朔儿金虫 (知名作家)
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【求助】grompp运行出错了，求解决方法！
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grompp运行出现的问题： 我做drug-enzyme的MD，力场选择gmx96，drug的gro、itp文件都是在prodrg2.5 server(bate)上得到的，大分子的top、gro文件是利用pdb2gmx得到的，我命令按一下方式进行：  editconf -f pro.gro -o pro_box.gro -bt cubic -box 15 15 15 genbox -cp pro_box.gro -cs spc216.gro -o pro_water.gro -p mix.top grompp -f em.mdp -c pro_water.gro -p mix.top -o pro_em.tpr 结果出现一下提示： error 0 [file "drg.itp",line 4] not enough parameters Fatal error:Bonded/nobonded atom type "1" not found! 下面是我用的mdp、pro.top和mix.top的部分信息： [pro.top] File 'pro.top' was generated ; By user: onbekend (0) ; On host: onbekend ; At date: Wed Nov 4 09:39:56 2009 ; ; This is your topology file ; "Lunatics On Pogo Sticks" (Red Hot Chili Peppers) ; ; Include forcefield parameters #include "ffG43a1.itp" [ moleculetype ] ; Name nrexcl Protein 3 [ atoms ] ; nr type resnr residue atom cgnr charge mass typeB chargeB massB 1 NL 1 ILE N 1 0.129 14.0067 ; qtot 0.129 2 H 1 ILE H1 1 0.248 1.008 ; qtot 0.377 3 H 1 ILE H2 1 0.248 1.008 ; qtot 0.625 4 H 1 ILE H3 1 0.248 1.008 ; qtot 0.873 5 CH1 1 ILE CA 1 0.127 13.019 ; qtot 1 ........ [ system ] ; Name Protein [ molecules ] ; Compound #mols Protein 1 [mdp] cpp = /lib/cpp define = -DFLEX_SPC constraints = none integrator = steep dt = 0.002 nsteps = 10000 ; 20ps nstlist = 10 optimize_fft = yes fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 coulombtype = pme pme_order = 4 ewald_rtol = 1e-5 ; ; Energy minimizing stuff ; emtol = 10 emstep = 0.01 nstcomm = 1 ns_type = grid rlist = 1.0 rcoulomb = 1.0 rvdw = 1.4 Tcoupl = no Pcoupl = no gen_vel = no [mix.top] File '1szr.top' was generated ; By user: onbekend (0) ; On host: onbekend ; At date: Wed Nov 4 09:39:56 2009 ; ; This is your topology file ; "Lunatics On Pogo Sticks" (Red Hot Chili Peppers) ; ; Include forcefield parameters #include "ffG43a1.itp" #include "drg.itp" [ moleculetype ] ; Name nrexcl Protein 3 [ atoms ] ; nr type resnr residue atom cgnr charge mass typeB chargeB massB 1 NL 1 ILE N 1 0.129 14.0067 ; qtot 0.129 2 H 1 ILE H1 1 0.248 1.008 ; qtot 0.377 ............ [ system ] ; Name Protein UNK [ molecules ] ; Compound #mols Protein 1 UNK 1 [drg.itp] ; ; ; This file was generated by PRODRG version AA081006.0504 ; PRODRG written/copyrighted by Daan van Aalten ; and Alexander Schuettelkopf ; ; Questions/comments to dava@davapc1.bioch.dundee.ac.uk ; ; When using this software in a publication, cite: ; A. W. Schuettelkopf and D. M. F. van Aalten (2004). ; PRODRG - a tool for high-throughput crystallography ; of protein-ligand complexes. ; Acta Crystallogr. D60, 1355--1363. ; ; [ moleculetype ] ; Name nrexcl UNK 3 [ atoms ] ; nr type resnr resid atom cgnr charge mass 1 CR1 1 UNK CBF 1 0.003 12.0110 2 HC 1 UNK HBF 1 0.035 1.0080 ............... [ bonds ] ; ai aj fu c0, c1, ... 1 2 2 0.109 12300000.0 0.109 12300000.0 ; CBF HBF 1 3 2 0.139 10800000.0 0.139 10800000.0 ; CBF CBG ............. [ pairs ] ; ai aj fu c0, c1, ... 1 6 1 ; CBF NBK 1 9 1 ; CBF CBI ................. [ angles ] ; ai aj ak fu c0, c1, ... 2 1 3 2 120.0 505.0 120.0 505.0 ; HBF CBF CBG 2 1 13 2 120.0 505.0 120.0 505.0 ; HBF CBF CBE ................ [ dihedrals ] ; ai aj ak al fu c0, c1, m, ... 1 13 3 2 2 0.0 167.4 0.0 167.4 ; imp CBF CBE CBG HBF 3 1 5 4 2 0.0 167.4 0.0 167.4 ; imp CBG CBF CBH HBG 请教上面的error怎么解决？另外我在pro.top中引入drg.itp生成mix.top，然后只给protein加入box和溶剂，利用mix.top进行grompp，这样的顺序对吗？愁死了，花费了几天还解决不了，非常感谢有人能帮忙！ [ Last edited by lei0736 on 2009-11-25 at 12:55 ] |
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易风朔儿
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