grompp 运行出错

我是一颗甜柠檬

在进行能量最小化的时候出现了Excluding 3 bonded neighbours molecule type 'Protein'Excluding 3 bonded neighbours molecule type 'DRG'
Excluding 2 bonded neighbours molecule type 'SOL'
Warning: atom name 64 in 1.top and 1_sol2.gro does not match (NAC - C)
Warning: atom name 65 in 1.top and 1_sol2.gro does not match (HAC - O)
Warning: atom name 66 in 1.top and 1_sol2.gro does not match (HAD - N)
Warning: atom name 67 in 1.top and 1_sol2.gro does not match (CAA - H)
Warning: atom name 68 in 1.top and 1_sol2.gro does not match (OAB - H)
Warning: atom name 69 in 1.top and 1_sol2.gro does not match (NAD - N)
Warning: atom name 70 in 1.top and 1_sol2.gro does not match (HAF - H)
Warning: atom name 71 in 1.top and 1_sol2.gro does not match (HAE - H)
Warning: atom name 72 in 1.top and 1_sol2.gro does not match (NAC - C)
Warning: atom name 73 in 1.top and 1_sol2.gro does not match (HAC - O)
Warning: atom name 74 in 1.top and 1_sol2.gro does not match (HAD - N)
Warning: atom name 75 in 1.top and 1_sol2.gro does not match (CAA - H)
Warning: atom name 76 in 1.top and 1_sol2.gro does not match (OAB - H)
Warning: atom name 77 in 1.top and 1_sol2.gro does not match (NAD - N)
Warning: atom name 78 in 1.top and 1_sol2.gro does not match (HAF - H)
Warning: atom name 79 in 1.top and 1_sol2.gro does not match (HAE - H)
Warning: atom name 80 in 1.top and 1_sol2.gro does not match (NAC - C)
Warning: atom name 81 in 1.top and 1_sol2.gro does not match (HAC - O)
Warning: atom name 82 in 1.top and 1_sol2.gro does not match (HAD - N)
Warning: atom name 83 in 1.top and 1_sol2.gro does not match (CAA - H)
(more than 20 non-matching atom names)

WARNING 1 [file 1.top, line 476]:
  1600 non-matching atom names
  atom names from 1.top will be used
  atom names from 1_sol2.gro will be ignored


Analysing residue names:
There are:    10    Protein residues
There are:   200      Other residues
There are:  6094      Water residues
Analysing Protein...
Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups...
Number of degrees of freedom in T-Coupling group rest is 59832.00
Largest charge group radii for Van der Waals: 0.202, 0.202 nm
Largest charge group radii for Coulomb:       0.202, 0.202 nm
Calculating fourier grid dimensions for X Y Z
Using a fourier grid of 52x52x52, spacing 0.112 0.112 0.112
Estimate for the relative computational load of the PME mesh part: 0.27
This run will generate roughly 2 Mb of data

There was 1 warning

-------------------------------------------------------
Program grompp, VERSION 4.6.5
Source code file: /build/buildd/gromacs-4.6.5/src/kernel/grompp.c, line: 1910

Fatal error:
Too many warnings (1), grompp terminated.
这样的错误提示，可是不知道要怎么样修改，请大神指点

我是一颗甜柠檬

wangpengfei 发表于 2016-7-21 22:09
配体的位置忘了加进复合物里了吧，小问题。

我是向体系当中加尿素和水，修改完拓扑文件之后就会运行出错，
; Include Position restraint file
#ifdef POSRES
#include "posre.itp"
#endif

; Include Ligand topology
#include "urea.itp"

;; Ligand position restraints
#ifdef POSRES
#include "posre_urea.itp"
#endif

; Include water topology
#include "gromos43a1.ff/spc.itp"

#ifdef POSRES_WATER
; Position restraint for each water oxygen
[ position_restraints ]
;  i funct       fcx        fcy        fcz
   1    1       1000       1000       1000
#endif

; Include topology for ions
#include "gromos43a1.ff/ions.itp"

[ system ]
; Name
Protein in water

[ molecules ]
; Compound        #mols
Protein             1
DRG               200
SOL              6094
这是我修改后的拓扑文件，请问有什么问题吗？

wangpengfei

wangpengfei 发表于 2016-7-21 22:58
复合溶剂我没做过也不太清楚该怎么做。但是既然你是按照普通的配体-受体体系做的，即使不怎么合适，理应也 ...

你看一下你的1_sol2.gro文件，原子从64开始是不是就变成了尿素了

我是一颗甜柠檬

wangpengfei 发表于 2016-7-21 22:41
目测gro文件里顺序不对，配体应该贴在蛋白质的下面

我做的不是蛋白质与配体复合，是想构建一个混合溶剂，是方法不对吗？（我要插入的尿素并不是一个，而是要添加好多个）

wangpengfei

gro文件和top文件不符，原子编号错误，自行检查编号修改正确即可

wangpengfei

wangpengfei 发表于 2016-7-21 22:08
gro文件和top文件不符，原子编号错误，自行检查编号修改正确即可

配体的位置忘了加进复合物里了吧，小问题。

wangpengfei

第一，命名和所指是否相符？
新手常犯的错误，比如说下下来的文件命名为xxx.itp，而实际上名称为drg.itp。你先检查名字是否一致。
第二，检查是否该贴进去的都贴进去了？构建complex的gro文件时配体加入了么？

wangpengfei

编号小的atom一般是蛋白质残基的，你的sol.gro里应该是尿素，检查一下顺序吧

wangpengfei

wangpengfei 发表于 2016-7-21 22:39
编号小的atom一般是蛋白质残基的，你的sol.gro里应该是尿素，检查一下顺序吧 ...

目测gro文件里顺序不对，配体应该贴在蛋白质的下面

我是一颗甜柠檬

wangpengfei 发表于 2016-7-21 22:39
编号小的atom一般是蛋白质残基的，你的sol.gro里应该是尿素，检查一下顺序吧 ...

sol.gro 里面有蛋白质，尿素和水

wangpengfei

复合溶剂我没做过也不太清楚该怎么做。但是既然你是按照普通的配体-受体体系做的，即使不怎么合适，理应也不该出现顺序上的错误。还是觉得哪个地方的顺序没有搞好。