双链能量最小化报错

Battleye

在能量最小化时出现以下错误：

WARNING: Listed nonbonded interaction between particles 6044 and 6051
at distance 2.914 which is larger than the table limit 2.000 nm.

This is likely either a 1,4 interaction, or a listed interaction inside
a smaller molecule you are decoupling during a free energy calculation.
Since interactions at distances beyond the table cannot be computed,
they are skipped until they are inside the table limit again. You will
only see this message once, even if it occurs for several interactions.

IMPORTANT: This should not happen in a stable simulation, so there is
probably something wrong with your system. Only change the table-extension
distance in the mdp file if you are really sure that is the reason.



WARNING: Listed nonbonded interaction between particles 3273 and 3280
at distance 2.915 which is larger than the table limit 2.000 nm.

This is likely either a 1,4 interaction, or a listed interaction inside
a smaller molecule you are decoupling during a free energy calculation.
Since interactions at distances beyond the table cannot be computed,
they are skipped until they are inside the table limit again. You will
only see this message once, even if it occurs for several interactions.

IMPORTANT: This should not happen in a stable simulation, so there is
probably something wrong with your system. Only change the table-extension
distance in the mdp file if you are really sure that is the reason.

经检查发现这两个原子分别位于双链的N端和C端，故猜测可能未区分AB链（pdb文件中未区分，但重新编号），但是我发现也生成了A链和B链，请问该如何修复

sobereva

不要自己手动在标题里写[GROMACS]这种标签，这次给你去了，以后注意

信息不充分没法判断。8成是拓扑文件问题或者和结构文件对应问题
反复检查。并且可以先尝试跑单链体系