最近參考 http://www.bevanlab.biochem.vt.e ... _protein/index.html
把自己研究的分子丟在DPPC上去模擬，使用的是GMX-4.0.4
我在"Orient the protein and membrane"這個階段遇到一些問題
照該網頁所言，要得到一個去PBC的DPPC結構，利用grompp&trjconv獲得gro檔
可我進行grompp時，卻得到一個不知怎麼處理的問題，以下是錯誤訊息:
[godkin@ncku-qe-x3550 MP-B]$ grompp -f minim.mdp -c dppc128.gro -p topol_dppc.top -o em.tpr
checking input for internal consistency...
processing topology...
Opening library file /home/godkin/Package/share/gromacs/top/ff_dum.itp
Generated 837 of the 2346 non-bonded parameter combinations
ERROR 1 [file dppc.itp, line 112]:
No default LJ-14 types
ERROR 2 [file dppc.itp, line 113]:
No default LJ-14 types
ERROR 3 [file dppc.itp, line 114]:
No default LJ-14 types
ERROR 4 [file dppc.itp, line 115]:
No default LJ-14 types
ERROR 5 [file dppc.itp, line 116]:
No default LJ-14 types
ERROR 6 [file dppc.itp, line 117]:
No default LJ-14 types
ERROR 7 [file dppc.itp, line 118]:
No default LJ-14 types
ERROR 8 [file dppc.itp, line 119]:
No default LJ-14 types
ERROR 9 [file dppc.itp, line 120]:
No default LJ-14 types
ERROR 10 [file dppc.itp, line 121]:
No default LJ-14 types
ERROR 11 [file dppc.itp, line 122]:
No default LJ-14 types
ERROR 12 [file dppc.itp, line 123]:
No default LJ-14 types
ERROR 13 [file dppc.itp, line 124]:
No default LJ-14 types
ERROR 14 [file dppc.itp, line 125]:
No default LJ-14 types
ERROR 15 [file dppc.itp, line 126]:
No default LJ-14 types
ERROR 16 [file dppc.itp, line 127]:
No default LJ-14 types
ERROR 17 [file dppc.itp, line 128]:
No default LJ-14 types
ERROR 18 [file dppc.itp, line 129]:
No default LJ-14 types
ERROR 19 [file dppc.itp, line 130]:
No default LJ-14 types
ERROR 20 [file dppc.itp, line 131]:
No default LJ-14 types
ERROR 21 [file dppc.itp, line 132]:
No default LJ-14 types
ERROR 22 [file dppc.itp, line 133]:
No default LJ-14 types
ERROR 23 [file dppc.itp, line 134]:
No default LJ-14 types
ERROR 24 [file dppc.itp, line 135]:
No default LJ-14 types
ERROR 25 [file dppc.itp, line 136]:
No default LJ-14 types
ERROR 26 [file dppc.itp, line 137]:
No default LJ-14 types
ERROR 27 [file dppc.itp, line 138]:
No default LJ-14 types
ERROR 28 [file dppc.itp, line 139]:
No default LJ-14 types
ERROR 29 [file dppc.itp, line 140]:
No default LJ-14 types
Opening library file /home/godkin/Package/share/gromacs/top/spc.itp
Opening library file /home/godkin/Package/share/gromacs/top/ions.itp
Excluding 3 bonded neighbours molecule type 'DPPC'
Excluding 2 bonded neighbours molecule type 'SOL'
processing coordinates...
double-checking input for internal consistency...
renumbering atomtypes...
converting bonded parameters...
-------------------------------------------------------
Program grompp, VERSION 4.0.4
Source code file: grompp.c, line: 986
Fatal error:
There were 29 errors in input file(s)
-------------------------------------------------------
"Welcome to the Power Age" (2 Unlimited)
請教各位大俠怎解?

请问你的dppc128.gro文件是怎么生成的呢？我现在也正做到这一步

你没有将lipid.itp中的pairtypes下的参数考到ffnonbond.itp里，没有好好看教程哦，o(∩_∩)o

我是用editconf -f dppc128.pdb -o dppc128.gro，不懂对不啊，还求大牛们指点~