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本帖最后由 牧生 于 2021-8-18 22:13 编辑
一、尝试做甲烷水合物的模拟，使用CrystalMaker直接生成一个甲烷水合物的pdb晶胞，
二、使用ligpargen在线得到甲烷的itp文件，把[ atomtypes ]内容剪切到ffnonbonded.itp，用opls力场，把forcefield.itp，ffnonbonded.itp等相关文件都复制到当前目录下
三、根据碳原子和氧原子的数量，手搓top文件为
#include "forcefield.itp"
;#include "tip4p-ice.itp"
#include "spce.itp" ;这里用的三点水模型，计划在能量最小化以后，再转为四点水模型
#include "jiawan.itp" ；其次才出现甲烷的itp
[ system ]
jiawan in water
[ molecules ]
; Compound nmols
SOL 2484 ;先出现水
jiawan 432 ；再出现甲烷
四、对这个水合物晶胞进行能量最小化，就报错：
Setting the LD random seed to 1566708099
Generated 337431 of the 337431 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 0.5
Generated 337431 of the 337431 1-4 parameter combinations
Excluding 2 bonded neighbours molecule type 'SOL'
Excluding 3 bonded neighbours molecule type 'jiawan'
Warning: atom name 1 in topol.top and 333.gro does not match (OW - C)
Warning: atom name 2 in topol.top and 333.gro does not match (HW1 - C)
Warning: atom name 3 in topol.top and 333.gro does not match (HW2 - C)
Warning: atom name 4 in topol.top and 333.gro does not match (OW - C)
Warning: atom name 5 in topol.top and 333.gro does not match (HW1 - C)
Warning: atom name 6 in topol.top and 333.gro does not match (HW2 - C)
Warning: atom name 7 in topol.top and 333.gro does not match (OW - C)
Warning: atom name 8 in topol.top and 333.gro does not match (HW1 - C)
Warning: atom name 9 in topol.top and 333.gro does not match (HW2 - C)
Warning: atom name 10 in topol.top and 333.gro does not match (OW - C)
Warning: atom name 11 in topol.top and 333.gro does not match (HW1 - C)
Warning: atom name 12 in topol.top and 333.gro does not match (HW2 - C)
Warning: atom name 13 in topol.top and 333.gro does not match (OW - C)
Warning: atom name 14 in topol.top and 333.gro does not match (HW1 - C)
Warning: atom name 15 in topol.top and 333.gro does not match (HW2 - C)
Warning: atom name 16 in topol.top and 333.gro does not match (OW - C)
Warning: atom name 17 in topol.top and 333.gro does not match (HW1 - C)
Warning: atom name 18 in topol.top and 333.gro does not match (HW2 - C)
Warning: atom name 19 in topol.top and 333.gro does not match (OW - C)
Warning: atom name 20 in topol.top and 333.gro does not match (HW1 - C)
(more than 20 non-matching atom names)
WARNING 1 [file topol.top, line 17]:
9612 non-matching atom names
atom names from topol.top will be used
atom names from 333.gro will be ignored
Removing all charge groups because cutoff-scheme=Verlet
Analysing residue names:
There are: 2484 Water residues
There are: 432 Other residues
Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups...
Number of degrees of freedom in T-Coupling group rest is 28833.00
Calculating fourier grid dimensions for X Y Z
Using a fourier grid of 60x32x32, spacing 0.118 0.111 0.111
Estimate for the relative computational load of the PME mesh part: 0.18
This run will generate roughly 57 Mb of data
There was 1 warning
-------------------------------------------------------
Program: gmx grompp, version 2019.6
Source file: src\gromacs\gmxpreprocess\grompp.cpp (line 2315)
Fatal error:
Too many warnings (1).
If you are sure all warnings are harmless, use the -maxwarn option.
但是看起来，top中，甲烷和水的顺序是对了的，为何原子名也是对不上的？
五、如果，我把top里面甲烷和水的位置换一下，会有如下报错（当然，我知道这个是因为顺序不对而报错）。
Setting the LD random seed to 368889344
Generated 337431 of the 337431 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 0.5
Generated 337431 of the 337431 1-4 parameter combinations
Excluding 3 bonded neighbours molecule type 'jiawan'
Excluding 2 bonded neighbours molecule type 'SOL'
Warning: atom name 1 in topol.top and 333.gro does not match (C00 - C)
Warning: atom name 2 in topol.top and 333.gro does not match (H01 - C)
Warning: atom name 3 in topol.top and 333.gro does not match (H02 - C)
Warning: atom name 4 in topol.top and 333.gro does not match (H03 - C)
Warning: atom name 5 in topol.top and 333.gro does not match (H04 - C)
Warning: atom name 6 in topol.top and 333.gro does not match (C00 - C)
Warning: atom name 7 in topol.top and 333.gro does not match (H01 - C)
Warning: atom name 8 in topol.top and 333.gro does not match (H02 - C)
Warning: atom name 9 in topol.top and 333.gro does not match (H03 - C)
Warning: atom name 10 in topol.top and 333.gro does not match (H04 - C)
Warning: atom name 11 in topol.top and 333.gro does not match (C00 - C)
Warning: atom name 12 in topol.top and 333.gro does not match (H01 - C)
Warning: atom name 13 in topol.top and 333.gro does not match (H02 - C)
Warning: atom name 14 in topol.top and 333.gro does not match (H03 - C)
Warning: atom name 15 in topol.top and 333.gro does not match (H04 - C)
Warning: atom name 16 in topol.top and 333.gro does not match (C00 - C)
Warning: atom name 17 in topol.top and 333.gro does not match (H01 - C)
Warning: atom name 18 in topol.top and 333.gro does not match (H02 - C)
Warning: atom name 19 in topol.top and 333.gro does not match (H03 - C)
Warning: atom name 20 in topol.top and 333.gro does not match (H04 - C)
(more than 20 non-matching atom names)
WARNING 1 [file topol.top, line 16]:
9612 non-matching atom names
atom names from topol.top will be used
atom names from 333.gro will be ignored
请大佬帮忙看看，为何这个pdb晶胞，在进行能量最小化这一步，原子名都对不上呢。如果强行忽略这个报错，那么能量最小化以后，晶体结构就散了。
附上所用的文件
em.mdp
(388 Bytes, 下载次数 Times of downloads: 53)
jiawan.itp
(1.36 KB, 下载次数 Times of downloads: 85)
topol.top
(200 Bytes, 下载次数 Times of downloads: 61)
ffnonbonded.itp
(62.01 KB, 下载次数 Times of downloads: 44)
ffbonded.itp
(204.7 KB, 下载次数 Times of downloads: 32)
forcefield.itp
(862 Bytes, 下载次数 Times of downloads: 33)
pdb文件略大，传到了蓝奏云，将后缀改为pdb即可https://wwa.lanzoui.com/i9fATstho8b
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发表于 Post on 2021-8-18 21:55:18
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