Fatal error molecule type sol contains no atoms gromacs

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Fatal error molecule type sol contains no atoms gromacs

Gromacs模拟一：配体-双链蛋白质复合物体系准

因为我觉得GROMACS官方英文教程和李继存老师的GROMACS的中文教程对于新手非常不友好,并且有很多细节的地方并没有详细说明,导致有很多困难的地方。这里记录一下自己成功的实验案例。书接上回,我们做完

Gromacs中遇到的各种报错以及警告合集_gromacs报错

在使用GROMACS进行多尺度仿真软件二次开发的过程中,开发者可能会遇到各种问题和故障。通过本节的介绍,希望开发者能够更好地理解这些问题,并掌握相应的解决方法

Common errors when using GROMACS — GROMACS 2018.1

T-Coupling group XXX has fewer than 10% of the atoms¶. It is possible to specify separate thermostats (temperature coupling groups) for every molecule type within a

Tutorial problem Protein-Ligand Complex

GROMACS version: 2020.2 GROMACS modification: No Hello, I am trying to follow the Protein-Ligand Complex tutorial but I end up in a problem and I don''t understand

[GROMACS] 求助No line with molecule type ''SOL'' found the

利用Gromacs做一个蛋白酶和两个配体的复合物模拟时,在添加离子过程中出现了以下错误： No line with molecule type ''SOL'' found the [molecule] section of file topol 。

[GROMACS] grompp出错Invalid order for directive

[ atomtypes ] [ system ] [ molecules ] 这几项只能出现一次。我的习惯是所有东西都写top文件里,不用itp文件。但也可以把两个itp 里面[ atomtypes ] 合并到一起写进一个新itp 文

Fatal error:No line with moleculetype ''SOL'' found the

文章浏览阅读2.6k次,点赞6次,收藏4次。在利用gromacs进行动力学模拟过程中,添加离子时出现报错信息：Fatal error:No line with moleculetype ''SOL'' found the

[GROMACS] 求助：使用gromacs进行添加离子的操作时

老师,我使用gromacs进行添加离子的操作时系统报错： No such moleculetype SOL。我使用sobtop进行了 p.gro的创建,然后使用gromacs进行溶剂化操作,系统提示

[GROMACS] 生成离子tpr文件时,提示No molecules were

模拟蛋白酶-小分子体系时,通过gmx grompp生成离子时,提示No molecules were defined in the system,检查了拓扑文件和gro文件都没有错误,请问各位大佬应该如何解决？其

[GROMACS] 添加离子时出错,atomtype na not found 求助

解决方案是：在小分子中将 [atomtypes]写入 [moleculetype]之前,之后仍然会出现atometype not found的报错,这是因为小分子力场和amber力场大小写不同导致,接下来将 [

如何修复GROMACS错误"没有这样的分子类型SOL"？

在添加离子的步骤中 (使用genion来生成ion.tpr文件),我得到了''No这类分子型SOL''。当我在分子类型部分添加SOL时,我得到''分子型''蛋白质没有原子''。任何帮助都是非

Grompp -r --does not match the number of atoms in the

Excluding 2 bonded neighbours molecule type ''SOL'' Excluding 1 bonded neighbours molecule type ''NA'' turning H bonds into constraints... NOTE 1 [file topol , line

Run-time errors — GROMACS 2016.4 documentation

Fatal error: No such moleculetype XXX¶ Each type of molecule in your [molecules] section of your top file must have a corresponding [moleculetype] section defined previously,

gromacs运行pdb2gmx指令出现问题

Fatal error: There were 4 missing atoms in molecule Protein_chain_A, if you want to use this incomplete topology anyhow, use the option -missing 下面分别贴上*.pdb和*.rtp文件

How to solve ERROR 1 [file topol , line 183055]: No such

I ran gromacs with command: grompp -f ions.mdp -c protein a_solv.gro -p topol -o ions.tpr. and yielded a Fatal error: Correct the number of coordinates in coordinate file (protein a.gro, 36891

Fatal error: There were 2 errors in input file (s)

No default Proper Dih. types. ERROR 2 [file sin p, line 344]: No default Proper Dih. types. Excluding 3 bonded neighbours molecule type ''Protein_chain_A'' Excluding 3

Common errors when using GROMACS

Fatal error: No such moleculetype XXX# Each type of molecule in your [molecules] section of your top file must have a corresponding [moleculetype] section defined previously,

gmx solvate crashing or leaving gaps for hexagonal solvent box

Solvent box contains 99373 atoms in 28208 residues Removed 12253 solvent atoms due to solvent-solvent overlap Removed 5122 solvent atoms due to solute-solvent

No such moleculetype ''SOL''

However, after the solvation stage, I keep encountering this error when I try to run the command: "gmx grompp -f ions.mdp -c solvated.gro -p topol -o ions.tpr" The error:

How to correct invalid atom type error in gromacs?

I am facing a problem between different versions of gromacs for gmx pdb2gmx. I have a protein-ligand system, I did all the necessary steps mentioned in gromacs manual for

[GROMACS] gromacs关于能量最小化出现警告的问题

请教各位老师,输入指令后提示这样的警告,不知道该怎么处理。 NOTE 1 [file minim.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the

[GROMACS] gmx加水时提示topol 中没有SOL组

"第16届北京科音分子动力学与GROMACS培训班" 将于5月3日至6日于北京举办。 Fatal error: No line with moleculetype ''SOL'' found the [ molecules ] section of file ''topol ''

chemistry

关于蛋白质错误 - 检查您的 *.gro 文件中是否包含 1 个蛋白质分子和 53832 个水分子。我怀疑你的 *.gro 文件没有蛋白质分子并且只装满了水。确保 topol 中的分子数应与

Molecule definition

When gen-pairs is set to no, grompp will give a warning for each pair type for which no parameters are given. The normal pair interactions, intended for 1-4 interactions,