| 查看: 3377 | 回复: 8 | ||
| 当前只显示满足指定条件的回帖，点击这里查看本话题的所有回帖 | ||
[求助]
topol文件不识别小分子 已有1人参与
|
||
|
最近刚刚学gromacs，按照网上的tutorial步骤走遇到一个问题就是我要添加我的小分子到pdb2gmx产生的conf.gro文件，我按照网上的tutorial添加需要的文件之后，还是不识别我的小分子，怎么办？我把topol文件里面的分子数手动修改之后，就出现下面的错误了 NOTE 1 [file topol.top, line 10673]: System has non-zero total charge: 6.000001e+00 Warning: atom name 1694 in topol.top and solv.gro does not match (CAA - AA) Warning: atom name 1695 in topol.top and solv.gro does not match (CAG - AG) Warning: atom name 1696 in topol.top and solv.gro does not match (CAH - AH) Warning: atom name 1697 in topol.top and solv.gro does not match (CAJ - AJ) Warning: atom name 1698 in topol.top and solv.gro does not match (CAF - AF) Warning: atom name 1699 in topol.top and solv.gro does not match (HAG - AG) Warning: atom name 1700 in topol.top and solv.gro does not match (CAD - AD) Warning: atom name 1701 in topol.top and solv.gro does not match (HAE - AE) Warning: atom name 1702 in topol.top and solv.gro does not match (CAC - AC) Warning: atom name 1703 in topol.top and solv.gro does not match (HAD - AD) Warning: atom name 1704 in topol.top and solv.gro does not match (CAE - AE) Warning: atom name 1705 in topol.top and solv.gro does not match (HAF - AF) Warning: atom name 1706 in topol.top and solv.gro does not match (CAI - AI) Warning: atom name 1707 in topol.top and solv.gro does not match (OAB - AB) Warning: atom name 1708 in topol.top and solv.gro does not match (HAL - AL) WARNING 1 [file topol.top, line 10673]: 15 non-matching atom names atom names from topol.top will be used atom names from solv.gro will be ignored NOTE 2 [file topol.top]: The largest charge group contains 11 atoms. Since atoms only see each other when the centers of geometry of the charge groups they belong to are within the cut-off distance, too large charge groups can lead to serious cut-off artifacts. For efficiency and accuracy, charge group should consist of a few atoms. For all-atom force fields use: CH3, CH2, CH, NH2, NH, OH, CO2, CO, etc. Analysing residue names: There are: 163 Protein residues There are: 1 Other residues There are: 10445 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 67791.00 Largest charge group radii for Van der Waals: 0.354, 0.287 nm Largest charge group radii for Coulomb: 0.354, 0.287 nm Calculating fourier grid dimensions for X Y Z Using a fourier grid of 72x72x72, spacing 0.109 0.109 0.109 Estimate for the relative computational load of the PME mesh part: 0.37 This run will generate roughly 383 Mb of data There were 2 notes There was 1 warning 这个怎么办？ |
回复此楼» 猜你喜欢
售SCI一区T0P文章，我:8O.55.1.O.5.4,科目齐全,可+急
已经有5人回复
-
售SCI-T0P文章，我:8O.5.5.1.O.54,科目齐全,可+急
已经有7人回复
-
上海工程技术大学 激光智能制造课题组 2027级博士研究生招生
已经有6人回复
-
课题组招2027级博士 上海工程技术大学 激光智能制造方向
已经有6人回复
-
现代”学阀”该如何界定
已经有14人回复
-
师弟论文见刊大半年才想起来申请专利，还能抢救一下吗？
已经有4人回复
-
有机合成以后会不会被AI改变？做科研的虫友怎么看
已经有8人回复
-
我的奶奶
已经有3人回复
» 本主题相关商家推荐: (我也要在这里推广)
» 本主题相关价值贴推荐，对您同样有帮助:
- 分子进化
已经有60人回复
- 有人遇到过MS文件读写错误的情况吗？
已经有4人回复
- 求助蛋白纯化的高手
已经有5人回复
- 求可以说明主客体分子识别的实验
已经有10人回复
- 15个金币求助投哪个期刊杂志（分子识别方面）
已经有4人回复
- QMolSymmetry:分子对称性识别，调整，优化（C++源码）
已经有6人回复
- 使用towhee进行GEMC模拟相平衡的MC运动定义问题..
已经有15人回复
- 如何入门有机中的分子识别或者离子识别或者阴阳离子受体等方向大讨论
已经有4人回复
- 【求助】玻璃化转变温度的识别
已经有20人回复
- 【转贴】识别图片PDF文件中的文字【已搜索无重复】
已经有16人回复
- CTEX2.8编辑的文件TEX/LATEX2.0识别吗
已经有6人回复
- 【求助】namd和vmd就只能识别.pdb.psf.coor.vel等文件吗
已经有6人回复
- 专题调查Understanding Molecular Simulation: from Algorithm to Application
已经有39人回复
4楼2011-12-31 08:59:14