amber在最后生成拓扑文件和坐标文件遇到报错

SuXXXX

各位老师，是这样的，我遇到两个问题：
1、''tleap -s -f 4j1w_tleap.in > 4j1w_tleap.out''
生成最终用来跑MD的拓扑文件（4j1w_solv.prmtop）和坐标文件（4j1w_solv.inpcrd）时，无Error，有warning，我无视了warning
"ambpdb -p 4j1w_solv.prmtop -c 4j1w_solv.inpcrd > A.pdb"
想用该方法合成pdb，手动检查结构，但出现报错：
“Error: Atom 5861 was assigned a lower molecule # (1) than previous atom (2).
Error:   This can happen if bond information is incorrect or missing, or if the
Error:   atom numbering in molecules is not sequential. Try one of the
Error:   following:
Error: - If this is a PDB file, try using the 'noconect' keyword.
Error: - If this topology did not have bond info, try increasing the bond
Error:   search cutoff above 0.2 Ang. ('bondsearch <cutoff>').
Error: - Use the 'fixatomorder' command to reorder the topology and any
Error:   associated coordinates.
Error: - Use the 'setMolecules' command in parmed to reorder only the
Error:   topology.
Error: Could not determine molecule information for 4j1w_solv.prmtop.
Error: SetSolventInfo: No molecule information.
Error: Could not determine solvent information for 4j1w_solv.prmtop.”

在查阅官网的教程(http://ambermd.org/tutorials/advanced/tutorial20/mcpbpy.htm)后，使用以下方法尝试解决问题：

输入“cpptraj -p 4j1w_solv.prmtop -c 4j1w_solv.inpcrd -i fixatord.in > fixatord.out”
依旧出现同样报错，且未生成fixed.4j1w_solv.prmtop和fixed.4j1w_solv.inpcrd文件，目前我不知道问题出在哪里，前面的操作我也找不到错处。


2、尽管重复多次，我一直有这样一个警告出现：
Warning: Amber topology flag 'CMAP_COUNT' is unrecognized and will be skipped.
Warning: Amber topology flag 'CMAP_RESOLUTION' is unrecognized and will be skipped.
Warning: Amber topology flag 'CMAP_PARAMETER_01' is unrecognized and will be skipped.
Warning: Amber topology flag 'CMAP_PARAMETER_02' is unrecognized and will be skipped.
Warning: Amber topology flag 'CMAP_PARAMETER_03' is unrecognized and will be skipped.
Warning: Amber topology flag 'CMAP_PARAMETER_04' is unrecognized and will be skipped.
Warning: Amber topology flag 'CMAP_PARAMETER_05' is unrecognized and will be skipped.
Warning: Amber topology flag 'CMAP_PARAMETER_06' is unrecognized and will be skipped.
Warning: Amber topology flag 'CMAP_PARAMETER_07' is unrecognized and will be skipped.
Warning: Amber topology flag 'CMAP_PARAMETER_08' is unrecognized and will be skipped.
Warning: Amber topology flag 'CMAP_PARAMETER_09' is unrecognized and will be skipped.
Warning: Amber topology flag 'CMAP_PARAMETER_10' is unrecognized and will be skipped.
Warning: Amber topology flag 'CMAP_PARAMETER_11' is unrecognized and will be skipped.
Warning: Amber topology flag 'CMAP_PARAMETER_12' is unrecognized and will be skipped.
Warning: Amber topology flag 'CMAP_PARAMETER_13' is unrecognized and will be skipped.
Warning: Amber topology flag 'CMAP_PARAMETER_14' is unrecognized and will be skipped.
Warning: Amber topology flag 'CMAP_INDEX' is unrecognized and will be skipped.
在对比了已经毕业的师姐(在其他学校的Linux上进行计算)做的酶，她的拓扑文件里确实没有CMAP_COUNT这些东西的出现，和我的不大一样，我的拓扑文件中会有CMAP_COUNT这些片段，她的不存在这样的警告，我也一直找不到问题的所在。
麻烦各位同行老师们了！

casea

1. 官网写的fixatord.in命令有问题，`trajout  fixed.1Y79_solv.inpcrd restart` restart需要放在最后
2. 使用tleap生成topol时可以直接生成pdb文件 `savepdb mol xxxx.pdb`

SuXXXX

casea 发表于 2022-8-24 08:55
1. 官网写的fixatord.in命令有问题，`trajout  fixed.1Y79_solv.inpcrd restart` restart需要放在最后
2.  ...

感谢老师的回复！但是我还是遇到了问题：
1、我将“trajout restart fixed.1Y79_solv.inpcrd ”更改为“trajout fixed.1Y79_solv.inpcrd restart”，依旧是一样的错误。
2、用tleap直接生成了pdb文件我检查了结构没有问题，但是如果将拓扑文件和坐标文件合成pdb结构文件，就出现错误，这是说明我的拓扑文件和坐标文件有问题吗。
麻烦老师了！

casea

SuXXXX 发表于 2022-8-24 09:41
感谢老师的回复！但是我还是遇到了问题：
1、我将“trajout restart fixed.1Y79_solv.inpcrd ”更改为“ ...

可能prmtop格式不兼容，可以手动把prmtop里面提示报错的字符段删除试试。我之前也遇到过，把那些topol flag及其包含内容删掉即可

SuXXXX

casea 发表于 2022-8-24 10:05
可能prmtop格式不兼容，可以手动把prmtop里面提示报错的字符段删除试试。我之前也遇到过，把那些topol fl ...

好的！！感谢您！！！